Variant report

Variant	rs320109
Chromosome Location	chr11:63680045-63680046
allele	A/C
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	chr11:63679946-63680136	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:63680017-63680226	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:63680032-63680575	K562	blood:	n/a	n/a
4	POLR2A	chr11:63680032-63680601	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr11:63678720-63680642	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:63679530-63680488	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:63679828-63680500	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:63673944..63681438-chr11:63681488..63685981,13	K562	blood:
2	chr11:63674570..63680304-chr11:63681753..63686803,9	MCF-7	breast:

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:45)

rs_ID	r²[population]
rs10736731	0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10792421	1.00[CEU][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs10792422	0.92[EUR][1000 genomes]
rs10792423	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10897452	0.88[EUR][1000 genomes]
rs10897453	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs10897454	1.00[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs10897459	0.85[JPT][hapmap]
rs11231600	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11231606	0.81[EUR][1000 genomes]
rs11231624	0.86[EUR][1000 genomes]
rs11231637	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11231640	0.89[CEU][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs11605500	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12277481	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12576275	0.91[EUR][1000 genomes]
rs12786124	0.85[JPT][hapmap]
rs1486936	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1872772	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2318126	0.85[JPT][hapmap]
rs2840079	0.89[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs3802941	0.92[CEU][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4143327	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs449047	0.85[JPT][hapmap]
rs454474	0.85[JPT][hapmap]
rs4980503	0.92[EUR][1000 genomes]
rs4980505	0.91[EUR][1000 genomes]
rs4980507	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4980528	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4980529	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4980530	0.85[JPT][hapmap]
rs4980532	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4980533	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]
rs6421686	0.89[EUR][1000 genomes]
rs6591825	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7102006	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7105288	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7108375	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7110843	0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7118913	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7121067	0.89[EUR][1000 genomes]
rs7937314	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7944519	1.00[CEU][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7948656	0.89[EUR][1000 genomes]
rs923247	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv1839119	chr11:63615554-63680052	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
rs320109	MS4A12	cis	parietal	SCAN
rs320109	HNRNPUL2	cis	parietal	SCAN
rs320109	SLC22A20	cis	parietal	SCAN
rs320109	SLC22A24	cis	parietal	SCAN
rs320109	CABP2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63659600-63680600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr11:63659800-63682400	Strong transcription	Fetal Intestine Large	intestine
3	chr11:63664600-63680400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:63669600-63683200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:63670000-63683200	Weak transcription	K562	blood
6	chr11:63670000-63683400	Weak transcription	HSMM	muscle
7	chr11:63670800-63681600	Weak transcription	GM12878-XiMat	blood
8	chr11:63671000-63681800	Weak transcription	HUVEC	blood vessel
9	chr11:63671000-63683800	Weak transcription	NHDF-Ad	bronchial
10	chr11:63672200-63682600	Weak transcription	HepG2	liver
11	chr11:63672200-63682600	Weak transcription	NH-A	brain
12	chr11:63672400-63683200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr11:63672400-63683800	Weak transcription	Psoas Muscle	Psoas
14	chr11:63673200-63680400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:63673200-63682600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:63673200-63683200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr11:63673800-63682800	Weak transcription	Osteobl	bone
18	chr11:63675800-63680200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:63676200-63683400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:63676400-63682800	Weak transcription	Right Atrium	heart
21	chr11:63676400-63683400	Weak transcription	Brain Substantia Nigra	brain
22	chr11:63676400-63683400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr11:63676600-63681200	Weak transcription	Brain Anterior Caudate	brain
24	chr11:63676600-63682600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:63676600-63682600	Weak transcription	Stomach Mucosa	stomach
26	chr11:63676600-63683400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:63676600-63683400	Weak transcription	Brain Angular Gyrus	brain
28	chr11:63676600-63684000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:63676600-63684000	Weak transcription	Aorta	Aorta
30	chr11:63676800-63682600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:63676800-63683200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:63676800-63683200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr11:63676800-63683200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:63676800-63683400	Weak transcription	HMEC	breast
35	chr11:63677000-63683400	Weak transcription	Hela-S3	cervix
36	chr11:63677000-63683600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr11:63677200-63680600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:63677400-63682600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:63677600-63682400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr11:63677600-63682400	Strong transcription	Fetal Intestine Small	intestine
41	chr11:63677600-63682600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:63677600-63683400	Weak transcription	Ovary	ovary
43	chr11:63677800-63680600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:63677800-63681400	Genic enhancers	Brain Germinal Matrix	brain
45	chr11:63677800-63682600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:63677800-63682600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:63677800-63682600	Weak transcription	Brain Hippocampus Middle	brain
48	chr11:63677800-63682600	Weak transcription	Esophagus	oesophagus
49	chr11:63677800-63683200	Weak transcription	Dnd41	blood
50	chr11:63677800-63683400	Weak transcription	Colon Smooth Muscle	Colon

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