Variant report

Variant	rs3212038
Chromosome Location	chr14:104178186-104178187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:104177585-104178332	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr14:104177060-104179960	U87	brain:	n/a	n/a
3	POLR2A	chr14:104177953-104179209	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr14:104178073-104180844	GM19193	blood:	n/a	n/a
5	POLR2A	chr14:104177685-104180996	K562	blood:	n/a	n/a
6	POLR2A	chr14:104176765-104181219	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr14:104178008-104180304	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr14:104178052-104178294	K562	blood:	n/a	n/a
9	POLR2A	chr14:104178170-104178756	U87	brain:	n/a	n/a
10	POLR2A	chr14:104178163-104178695	ProgFib	skin:	n/a	n/a
11	POLR2A	chr14:104178161-104178361	GM12878	blood:	n/a	n/a
12	POLR2A	chr14:104177945-104178343	GM12878	blood:	n/a	n/a
13	POLR2A	chr14:104178034-104178407	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr14:104178139-104178527	HepG2	liver:	n/a	n/a
15	ZNF263	chr14:104177605-104178748	HEK293-T-REx	kidney:	n/a	n/a
16	POLR2A	chr14:104178141-104178895	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr14:104178166-104180750	GM12892	blood:	n/a	n/a
18	POLR2A	chr14:104177166-104181233	K562	blood:	n/a	n/a
19	POLR2A	chr14:104177298-104178761	A549	lung:	n/a	n/a
20	POLR2A	chr14:104178070-104178962	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr14:104178031-104178665	GM12891	blood:	n/a	n/a
22	POLR2A	chr14:104177162-104180671	HepG2	liver:	n/a	n/a
23	POLR2A	chr14:104177060-104179833	U87	brain:	n/a	n/a
24	POLR2A	chr14:104177892-104179032	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr14:104177932-104178529	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr14:104177943-104181042	HL-60	blood:	n/a	n/a
27	POLR2A	chr14:104177974-104178588	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr14:104178083-104180769	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr14:104177336-104180928	GM12892	blood:	n/a	n/a
30	POLR2A	chr14:104177965-104178387	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr14:104177987-104180767	GM12878	blood:	n/a	n/a
32	POLR2A	chr14:104177645-104180774	GM12892	blood:	n/a	n/a
33	POLR2A	chr14:104177907-104178515	GM12891	blood:	n/a	n/a
34	POLR2A	chr14:104178179-104178218	MCF-7	breast:	n/a	n/a
35	POLR2A	chr14:104177935-104178582	GM12878	blood:	n/a	n/a
36	POLR2A	chr14:104177466-104180933	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr14:104177263-104180149	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:104094610..104096385-chr14:104176505..104178992,4	MCF-7	breast:
2	chr14:103992666..103995489-chr14:104177229..104179572,2	MCF-7	breast:
3	chr14:104177501..104178382-chr2:232328527..232329361,2	Hela-S3	cervix:
4	chr14:103994810..103997176-chr14:104176629..104178794,2	MCF-7	breast:

No data

Variant related genes	Relation type
XRCC3	TF binding region
ZFYVE21	TF binding region
ENSG00000269963	TF binding region
ENSG00000126214	Chromatin interaction
ENSG00000260285	Chromatin interaction
ENSG00000166166	Chromatin interaction
ENSG00000115053	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11540512	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11844466	0.81[AFR][1000 genomes]
rs11846404	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11846838	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11851616	0.81[AFR][1000 genomes]
rs12147645	0.89[EUR][1000 genomes]
rs12590968	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12884809	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12888993	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12892038	0.81[AFR][1000 genomes]
rs12896171	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1606	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1799796	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273175	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2295152	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212024	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212076	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212090	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34000399	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34843146	0.81[AFR][1000 genomes]
rs35011804	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35921969	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4525427	0.81[AFR][1000 genomes]
rs4900590	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4900591	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4900592	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4906350	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4906356	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7148857	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs729438	0.81[AFR][1000 genomes]
rs8021229	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
6	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv902308	chr14:104087209-104211180	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv1041329	chr14:104097750-104196346	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv542202	chr14:104097750-104196346	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1048866	chr14:104100862-104195896	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
12	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
13	nsv1041347	chr14:104141217-104186372	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
14	nsv902309	chr14:104143385-104198251	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
15	nsv902310	chr14:104143385-104205811	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
16	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
17	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
18	nsv902311	chr14:104148339-104205811	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
19	nsv902312	chr14:104155317-104211180	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
20	esv1796914	chr14:104159882-104181369	Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
21	nsv527425	chr14:104162263-104198251	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
22	nsv470673	chr14:104162263-104219949	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
23	nsv902313	chr14:104162263-104378087	Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
24	nsv902315	chr14:104165927-104190527	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
25	nsv902316	chr14:104173823-104195161	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
26	nsv902317	chr14:104175676-104194278	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3212038	RP11-73M18.8	cis	Whole Blood	GTEx
rs3212038	KLC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104152600-104178600	Weak transcription	Small Intestine	intestine
2	chr14:104161200-104180000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr14:104161200-104180400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr14:104164200-104178600	Weak transcription	Fetal Heart	heart
5	chr14:104165400-104180400	Strong transcription	Thymus	Thymus
6	chr14:104167200-104179600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr14:104169000-104180200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr14:104172000-104178200	Weak transcription	NHDF-Ad	bronchial
9	chr14:104172000-104178600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr14:104172600-104180600	Weak transcription	Primary B cells from cord blood	blood
11	chr14:104173000-104178600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr14:104173000-104179600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr14:104173000-104180400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr14:104174200-104179800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr14:104174200-104180000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr14:104174600-104180400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr14:104174800-104179800	Enhancers	Stomach Mucosa	stomach
18	chr14:104174800-104180400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr14:104175000-104180600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr14:104175200-104180000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr14:104175200-104180600	Weak transcription	Fetal Lung	lung
22	chr14:104175200-104181000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr14:104175400-104178200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr14:104175400-104179600	Weak transcription	K562	blood
25	chr14:104175600-104180400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr14:104175800-104178200	Weak transcription	Colon Smooth Muscle	Colon
27	chr14:104175800-104180400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr14:104175800-104180800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr14:104176000-104180600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr14:104176200-104180400	Weak transcription	Fetal Brain Female	brain
31	chr14:104176400-104180200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr14:104176400-104180600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr14:104176400-104180600	Weak transcription	Brain Angular Gyrus	brain
34	chr14:104176400-104180800	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr14:104176600-104179200	Enhancers	Duodenum Mucosa	Duodenum
36	chr14:104176800-104180000	Weak transcription	Fetal Thymus	thymus
37	chr14:104177000-104180000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr14:104177200-104178400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr14:104177200-104178600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr14:104177200-104178800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr14:104177200-104178800	Enhancers	Brain Hippocampus Middle	brain
42	chr14:104177200-104179000	Enhancers	HUVEC	blood vessel
43	chr14:104177200-104179600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr14:104177200-104180400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
45	chr14:104177400-104178200	Enhancers	HSMMtube	muscle
46	chr14:104177400-104178400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr14:104177400-104179000	Enhancers	H1 Cell Line	embryonic stem cell
48	chr14:104177400-104179000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr14:104177400-104179000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr14:104177400-104179000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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