Variant report

Variant	rs861545
Chromosome Location	chr14:104155945-104155946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:104155049-104158914	GM12891	blood:	n/a	n/a
2	POLR2A	chr14:104154781-104156308	A549	lung:	n/a	n/a
3	POLR2A	chr14:104155660-104156351	GM12891	blood:	n/a	n/a
4	POLR2A	chr14:104155918-104156211	GM12878	blood:	n/a	n/a
5	POLR2A	chr14:104155923-104156019	ProgFib	skin:	n/a	n/a
6	POLR2A	chr14:104155047-104156112	HepG2	liver:	n/a	n/a
7	IRF1	chr14:104155847-104155991	K562	blood:	n/a	n/a
8	POLR2A	chr14:104155287-104157078	GM12878	blood:	n/a	n/a
9	SP1	chr14:104155845-104156224	GM12878	blood:	n/a	n/a
10	PML	chr14:104155159-104156311	GM12878	blood:	n/a	n/a
11	POLR2A	chr14:104155508-104156399	GM12891	blood:	n/a	n/a
12	TAF1	chr14:104155911-104156130	GM12878	blood:	n/a	n/a
13	POLR2A	chr14:104155774-104156346	GM12878	blood:	n/a	n/a
14	POLR2A	chr14:104154865-104156285	K562	blood:	n/a	n/a
15	SP1	chr14:104155791-104156278	GM12878	blood:	n/a	n/a
16	MTA3	chr14:104155531-104156319	GM12878	blood:	n/a	n/a
17	EBF1	chr14:104155545-104156179	GM12878	blood:	n/a	n/a
18	TAF1	chr14:104155851-104156274	GM12878	blood:	n/a	n/a
19	POLR2A	chr14:104155499-104156443	GM12891	blood:	n/a	n/a
20	WRNIP1	chr14:104155419-104156228	GM12878	blood:	n/a	n/a
21	POLR2A	chr14:104155877-104156240	GM12878	blood:	n/a	n/a
22	USF2	chr14:104155601-104156268	GM12878	blood:	n/a	n/a
23	POLR2A	chr14:104154663-104156224	Hela-S3	cervix:	n/a	n/a
24	CHD1	chr14:104155587-104156293	GM12878	blood:	n/a	n/a
25	MAZ	chr14:104155610-104156162	GM12878	blood:	n/a	chr14:104156105-104156118 chr14:104156107-104156116 chr14:104156107-104156117 chr14:104156105-104156118 chr14:104156106-104156117 chr14:104156108-104156117 chr14:104156106-104156117 chr14:104156106-104156117 chr14:104156109-104156116 chr14:104156105-104156118
26	POLR2A	chr14:104155350-104156434	GM12878	blood:	n/a	n/a
27	POLR2A	chr14:104155242-104156301	GM12878	blood:	n/a	n/a
28	POU2F2	chr14:104155517-104156316	GM12878	blood:	n/a	n/a
29	MAX	chr14:104155551-104156280	GM12878	blood:	n/a	chr14:104156105-104156118 chr14:104156107-104156116 chr14:104156107-104156117 chr14:104156105-104156118 chr14:104156106-104156117 chr14:104156108-104156117 chr14:104156106-104156117 chr14:104156106-104156117 chr14:104156109-104156116 chr14:104156105-104156118
30	MXI1	chr14:104155544-104156279	GM12878	blood:	n/a	n/a
31	POU2F2	chr14:104155825-104156270	GM12891	blood:	n/a	n/a
32	POLR2A	chr14:104155834-104156256	GM12891	blood:	n/a	n/a
33	BHLHE40	chr14:104155633-104156231	GM12878	blood:	n/a	n/a
34	POLR2A	chr14:104155278-104157434	GM12878	blood:	n/a	n/a
35	TBP	chr14:104155521-104156236	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:104155176..104156837-chr14:104158255..104161002,2	K562	blood:
2	chr14:104153451..104157331-chr14:104158433..104160697,4	MCF-7	breast:
3	chr14:104155124..104157299-chr14:104157820..104159666,2	K562	blood:
4	chr14:104151812..104156751-chr14:104171759..104176142,6	K562	blood:
5	chr14:104151853..104154056-chr14:104155679..104158649,2	K562	blood:
6	chr14:104154470..104157161-chr14:104195368..104197500,2	K562	blood:

Variant related genes	Relation type
KLC1	TF binding region
ENSG00000269940	TF binding region
ENSG00000126215	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000126214	Chromatin interaction
ENSG00000270108	Chromatin interaction
ENSG00000269940	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10047805	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10131067	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11160756	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11625397	0.82[JPT][hapmap]
rs11850979	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2296483	0.82[JPT][hapmap]
rs2403202	0.82[CEU][hapmap]
rs2403203	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2896489	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35015260	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3742463	0.82[AMR][1000 genomes]
rs3742465	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3759586	0.86[CEU][hapmap];0.96[JPT][hapmap]
rs4900586	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4900589	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4906348	0.82[AMR][1000 genomes]
rs4906355	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4906358	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55647815	0.81[ASN][1000 genomes]
rs709399	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7154572	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs729437	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs745079	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs752624	0.82[JPT][hapmap]
rs8003289	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8007489	0.95[JPT][hapmap]
rs8007903	0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs8007915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8008451	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8021368	0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs8021904	0.83[AMR][1000 genomes]
rs861530	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs861537	0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs861544	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs861547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8702	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs861545	ENSG00000100711	cis	multi-tissue	Pritchard
rs861545	ZFYVE21	Cis_1M	lymphoblastoid	RTeQTL
rs861545	ZFYVE21	cis	multi-tissue	Pritchard
rs861545	ZFYVE21	cis	Lymphoblastoid	GTEx
rs861545	BAG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104097400-104156600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:104117800-104157000	Strong transcription	Dnd41	blood
3	chr14:104117800-104176000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr14:104118800-104175600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:104119200-104173000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr14:104119400-104157000	Strong transcription	Fetal Thymus	thymus
7	chr14:104119400-104161800	Strong transcription	Fetal Intestine Small	intestine
8	chr14:104119400-104164600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr14:104119400-104175200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr14:104120000-104177000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr14:104120200-104161400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr14:104120200-104161800	Strong transcription	Fetal Intestine Large	intestine
13	chr14:104120400-104157000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr14:104120400-104157000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr14:104120400-104161200	Strong transcription	Fetal Stomach	stomach
16	chr14:104120800-104157200	Strong transcription	Thymus	Thymus
17	chr14:104121000-104162000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:104124600-104169800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr14:104124600-104169800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr14:104130600-104159600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr14:104131000-104161800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr14:104132800-104156000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr14:104133400-104177200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr14:104133800-104157000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr14:104134000-104156400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr14:104134000-104157000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr14:104134000-104157000	Strong transcription	Primary T cells from cord blood	blood
28	chr14:104134200-104156800	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr14:104134200-104157200	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr14:104134200-104161600	Strong transcription	NHDF-Ad	bronchial
31	chr14:104135600-104177600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr14:104139800-104164400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr14:104143600-104158600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr14:104143600-104162400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr14:104145400-104157200	Strong transcription	A549	lung
36	chr14:104146000-104157000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr14:104146000-104161400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr14:104146200-104157000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr14:104146200-104157200	Strong transcription	HSMMtube	muscle
40	chr14:104146200-104174800	Weak transcription	K562	blood
41	chr14:104147800-104159800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr14:104148600-104156200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr14:104149000-104156000	Strong transcription	HUVEC	blood vessel
44	chr14:104149200-104156400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr14:104149200-104157200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr14:104149200-104164600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr14:104149800-104159200	Weak transcription	Stomach Mucosa	stomach
48	chr14:104150200-104157400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr14:104151200-104156200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr14:104151400-104161800	Strong transcription	Muscle Satellite Cultured Cells	--

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