Variant report

Variant	rs4980533
Chromosome Location	chr11:63681648-63681649
allele	A/G
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	chr11:63681329-63682044	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:63681342-63683085	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:63681075-63681737	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr11:63681329-63681685	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr11:63681429-63681710	K562	blood:	n/a	n/a
6	POLR2A	chr11:63681309-63681878	MCF-7	breast:	n/a	n/a
7	POLR2A	chr11:63681363-63681968	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr11:63681626-63681786	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:63680773..63683406-chr11:63684086..63687112,3	MCF-7	breast:
2	chr11:63673944..63681438-chr11:63681488..63685981,13	K562	blood:

Variant related genes	Relation type
RCOR2	TF binding region
ENSG00000167771	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10736731	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10751001	0.85[ASN][1000 genomes]
rs10792421	0.81[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10792422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10792423	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10897452	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10897453	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10897454	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231600	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11231624	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11231628	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11231637	0.92[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11231640	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11231646	0.86[CHB][hapmap]
rs11605500	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12277481	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12576275	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1486936	0.92[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1872772	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2318110	0.83[ASN][1000 genomes]
rs2840079	0.86[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs320109	0.92[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3802941	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850943	0.85[ASN][1000 genomes]
rs4143327	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4963433	0.85[ASN][1000 genomes]
rs4980503	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4980505	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4980507	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4980528	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4980529	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4980532	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6421686	0.87[EUR][1000 genomes]
rs6591825	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7102006	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7105288	0.92[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7108375	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7110843	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7118913	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7121067	0.94[EUR][1000 genomes]
rs7937314	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7939416	0.80[ASN][1000 genomes]
rs7944519	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7948656	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs923247	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs928948	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[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	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv468589	chr11:63515752-63713239	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv555180	chr11:63515752-63713239	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS 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	39 gene(s)	inside rSNPs	diseases
4	nsv468590	chr11:63639881-63783352	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv555181	chr11:63639881-63783352	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv897629	chr11:63664882-63866959	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
9	nsv897632	chr11:63670787-63688693	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv897633	chr11:63670787-63691049	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv897634	chr11:63670787-63698538	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv897635	chr11:63674926-63688693	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv897636	chr11:63676067-63688693	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv897637	chr11:63676067-63691049	Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv897638	chr11:63676562-63688693	Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4980533	SLC22A24	cis	parietal	SCAN
rs4980533	MS4A12	cis	parietal	SCAN
rs4980533	SLC22A20	cis	parietal	SCAN
rs4980533	HNRNPUL2	cis	parietal	SCAN
rs4980533	CABP2	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63659800-63682400	Strong transcription	Fetal Intestine Large	intestine
2	chr11:63669600-63683200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:63670000-63683200	Weak transcription	K562	blood
4	chr11:63670000-63683400	Weak transcription	HSMM	muscle
5	chr11:63671000-63681800	Weak transcription	HUVEC	blood vessel
6	chr11:63671000-63683800	Weak transcription	NHDF-Ad	bronchial
7	chr11:63672200-63682600	Weak transcription	HepG2	liver
8	chr11:63672200-63682600	Weak transcription	NH-A	brain
9	chr11:63672400-63683200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:63672400-63683800	Weak transcription	Psoas Muscle	Psoas
11	chr11:63673200-63682600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr11:63673200-63683200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:63673800-63682800	Weak transcription	Osteobl	bone
14	chr11:63676200-63683400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:63676400-63682800	Weak transcription	Right Atrium	heart
16	chr11:63676400-63683400	Weak transcription	Brain Substantia Nigra	brain
17	chr11:63676400-63683400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:63676600-63682600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:63676600-63682600	Weak transcription	Stomach Mucosa	stomach
20	chr11:63676600-63683400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:63676600-63683400	Weak transcription	Brain Angular Gyrus	brain
22	chr11:63676600-63684000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:63676600-63684000	Weak transcription	Aorta	Aorta
24	chr11:63676800-63682600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr11:63676800-63683200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:63676800-63683200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr11:63676800-63683200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:63676800-63683400	Weak transcription	HMEC	breast
29	chr11:63677000-63683400	Weak transcription	Hela-S3	cervix
30	chr11:63677000-63683600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr11:63677400-63682600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:63677600-63682400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr11:63677600-63682400	Strong transcription	Fetal Intestine Small	intestine
34	chr11:63677600-63682600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr11:63677600-63683400	Weak transcription	Ovary	ovary
36	chr11:63677800-63682600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:63677800-63682600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr11:63677800-63682600	Weak transcription	Brain Hippocampus Middle	brain
39	chr11:63677800-63682600	Weak transcription	Esophagus	oesophagus
40	chr11:63677800-63683200	Weak transcription	Dnd41	blood
41	chr11:63677800-63683400	Weak transcription	Colon Smooth Muscle	Colon
42	chr11:63677800-63683400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr11:63678000-63682200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:63678000-63682400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:63678000-63682600	Weak transcription	Adipose Nuclei	Adipose
46	chr11:63678000-63682800	Weak transcription	NHEK	skin
47	chr11:63678000-63683200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr11:63678000-63683200	Weak transcription	Thymus	Thymus
49	chr11:63678000-63683200	Weak transcription	NHLF	lung
50	chr11:63678000-63683400	Weak transcription	Liver	Liver

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