Variant report

Variant	rs6542048
Chromosome Location	chr2:113032212-113032213
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:113032023-113032406	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr2:113032115-113032375	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:113031975-113032479	K562	blood:	n/a	n/a
4	POLR2A	chr2:113031520-113032468	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:113032012-113034316	K562	blood:	n/a	n/a
6	POLR2A	chr2:113032033-113032225	GM12878	blood:	n/a	n/a
7	ZNF384	chr2:113030208-113034002	K562	blood:	n/a	n/a
8	POLR2A	chr2:113032114-113032212	A549	lung:	n/a	n/a
9	PAX5	chr2:113032108-113032296	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:113031559-113034088	K562	blood:	n/a	n/a
11	POLR2A	chr2:113031072-113032452	K562	blood:	n/a	n/a
12	POLR2A	chr2:113032025-113034274	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:113032046-113034210	HepG2	liver:	n/a	n/a
14	HEY1	chr2:113032003-113032467	K562	blood:	n/a	n/a
15	POLR2A	chr2:113032032-113032452	GM12892	blood:	n/a	n/a
16	HEY1	chr2:113031996-113032237	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:113031714-113034350	GM12891	blood:	n/a	n/a
18	GTF3C2	chr2:113031498-113032390	K562	blood:	n/a	n/a
19	POLR2A	chr2:113031982-113032498	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:113032064-113032474	GM12892	blood:	n/a	n/a
21	POLR2A	chr2:113032133-113032266	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113031252..113036924-chr2:113235926..113242226,12	K562	blood:
2	chr2:113031538..113036695-chr2:113297613..113301921,6	K562	blood:
3	chr2:113031437..113035560-chr2:113235674..113241590,9	K562	blood:
4	chr2:113008666..113014085-chr2:113030385..113035561,7	MCF-7	breast:
5	chr2:113031915..113033704-chr7:75986232..75988777,2	K562	blood:
6	chr2:113030887..113033164-chr2:113520392..113522307,2	K562	blood:
7	chr2:113031655..113033342-chr2:113967822..113970476,2	K562	blood:
8	chr2:113031869..113034952-chr2:113341167..113343629,3	MCF-7	breast:
9	chr2:113010163..113016150-chr2:113027955..113035093,25	K562	blood:
10	chr2:112879135..112881392-chr2:113031053..113032839,3	K562	blood:
11	chr2:113009256..113015419-chr2:113031181..113035814,11	MCF-7	breast:
12	chr2:113031588..113034484-chr2:113102679..113104264,2	MCF-7	breast:
13	chr2:113031677..113034717-chr2:113042895..113047019,4	K562	blood:
14	chr2:113030987..113032908-chr2:113341896..113344079,2	K562	blood:
15	chr2:113032082..113034086-chr20:56283174..56285192,2	MCF-7	breast:
16	chr2:113031185..113034291-chr2:113402354..113405026,3	K562	blood:

No data

Variant related genes	Relation type
ZC3H6	TF binding region
ENSG00000238951	TF binding region
ENSG00000144161	Chromatin interaction
ENSG00000114999	Chromatin interaction
ENSG00000169607	Chromatin interaction
ENSG00000124225	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000235258	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000236555	Chromatin interaction
ENSG00000170027	Chromatin interaction
ENSG00000189223	Chromatin interaction
ENSG00000125611	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10167090	0.85[ASN][1000 genomes]
rs10169159	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10175234	0.94[ASN][1000 genomes]
rs10177573	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10183121	0.87[ASN][1000 genomes]
rs10203843	0.86[AFR][1000 genomes]
rs10205038	0.89[ASN][1000 genomes]
rs10864903	0.87[AFR][1000 genomes]
rs11123131	0.81[ASN][1000 genomes]
rs11123132	0.82[ASN][1000 genomes]
rs11674953	0.87[ASN][1000 genomes]
rs11688418	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11689487	0.94[ASN][1000 genomes]
rs11691431	0.89[ASN][1000 genomes]
rs11691794	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11896500	0.86[AFR][1000 genomes]
rs11903741	0.86[AFR][1000 genomes]
rs11904424	0.83[AFR][1000 genomes]
rs12464478	0.86[AFR][1000 genomes]
rs12711737	0.88[ASN][1000 genomes]
rs12711738	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13407329	0.81[ASN][1000 genomes]
rs34623958	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4258804	0.82[AFR][1000 genomes]
rs4332934	0.88[AFR][1000 genomes]
rs4392265	0.99[ASN][1000 genomes]
rs4399734	0.81[AFR][1000 genomes]
rs4430968	0.88[AFR][1000 genomes]
rs4446076	0.99[ASN][1000 genomes]
rs4450606	0.88[AFR][1000 genomes]
rs4456711	0.86[AFR][1000 genomes]
rs4522611	0.81[AFR][1000 genomes]
rs4539797	0.88[AFR][1000 genomes]
rs4622729	0.81[AFR][1000 genomes]
rs4849056	0.86[ASN][1000 genomes]
rs4849057	0.87[ASN][1000 genomes]
rs58337061	0.86[AFR][1000 genomes]
rs6542045	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542050	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6542051	0.87[AFR][1000 genomes]
rs6706874	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6708164	0.81[AFR][1000 genomes]
rs6716010	0.97[ASN][1000 genomes]
rs6745942	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs71414636	0.90[ASN][1000 genomes]
rs72831684	0.99[ASN][1000 genomes]
rs7557281	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7564052	0.83[AFR][1000 genomes]
rs7569894	0.81[AFR][1000 genomes]
rs7571435	0.87[ASN][1000 genomes]
rs7601888	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv874868	chr2:113021811-113076095	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv874869	chr2:113021811-113089267	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv874872	chr2:113027569-113070889	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv874873	chr2:113027569-113083367	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv874874	chr2:113027569-113089267	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113025200-113032600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:113026800-113032600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:113031200-113032400	Enhancers	Dnd41	blood
4	chr2:113031400-113032400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:113031400-113032400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:113031400-113032400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:113031400-113034600	Active TSS	K562	blood
8	chr2:113031600-113032400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr2:113031600-113032600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:113031800-113032400	Enhancers	Primary B cells from cord blood	blood
11	chr2:113031800-113034000	Active TSS	HUVEC	blood vessel
12	chr2:113032000-113032400	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:113032000-113032400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:113032000-113032400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:113032000-113032400	Enhancers	Fetal Brain Male	brain
16	chr2:113032000-113032400	Enhancers	GM12878-XiMat	blood
17	chr2:113032000-113032400	Enhancers	HepG2	liver
18	chr2:113032000-113032600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr2:113032000-113034200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:113032000-113034400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:113032000-113034400	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr2:113032000-113034800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:113032000-113035200	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr2:113032200-113032400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:113032200-113032400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:113032200-113032400	Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr2:113032200-113032400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:113032200-113032400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:113032200-113032400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr2:113032200-113032400	Enhancers	Stomach Smooth Muscle	stomach
31	chr2:113032200-113032600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:113032200-113032600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr2:113032200-113032600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr2:113032200-113032600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:113032200-113032600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr2:113032200-113032600	Enhancers	Spleen	Spleen
37	chr2:113032200-113032800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:113032200-113034000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:113032200-113034000	Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr2:113032200-113034200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:113032200-113034200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:113032200-113034200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:113032200-113034200	Active TSS	Liver	Liver
44	chr2:113032200-113034200	Active TSS	Brain Anterior Caudate	brain
45	chr2:113032200-113034400	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr2:113032200-113034400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:113032200-113034400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:113032200-113034400	Active TSS	Fetal Intestine Large	intestine
49	chr2:113032200-113034600	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr2:113032200-113034800	Active TSS	H1 Cell Line	embryonic stem cell

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