Variant report

Variant	rs7975331
Chromosome Location	chr12:11707231-11707232
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	RCOR1	chr12:11706648-11707329	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:11706778-11710160	GM12891	blood:	n/a	n/a
3	CTCF	chr12:11706872-11707282	A549	lung:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
4	CTCF	chr12:11706817-11707321	MCF-7	breast:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
5	RAD21	chr12:11706843-11707335	IMR90	lung:	n/a	chr12:11707059-11707078
6	POLR2A	chr12:11706837-11708074	GM12891	blood:	n/a	n/a
7	TBL1XR1	chr12:11706991-11707366	GM12878	blood:	n/a	n/a
8	MAZ	chr12:11706780-11707282	GM12878	blood:	n/a	n/a
9	RAD21	chr12:11706804-11707385	MCF-7	breast:	n/a	chr12:11707059-11707078
10	TAF1	chr12:11706972-11707282	GM12891	blood:	n/a	n/a
11	CTCF	chr12:11706931-11707246	Lung_OC	lung:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
12	RUNX3	chr12:11706697-11707385	GM12878	blood:	n/a	n/a
13	ZNF384	chr12:11706610-11707295	GM12878	blood:	n/a	n/a
14	CTCF	chr12:11706643-11707978	A549	lung:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
15	SMC3	chr12:11706900-11707236	HepG2	liver:	n/a	chr12:11707060-11707074
16	SMC3	chr12:11706733-11707694	GM12878	blood:	n/a	chr12:11707060-11707074
17	BHLHE40	chr12:11706817-11707347	GM12878	blood:	n/a	n/a
18	CTCF	chr12:11706800-11707302	GM12878	blood:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
19	POLR2A	chr12:11706995-11707371	GM12891	blood:	n/a	n/a
20	CTCF	chr12:11706835-11707305	MCF-7	breast:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
21	REST	chr12:11706979-11707271	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr12:11706840-11707280	IMR90	lung:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
23	RAD21	chr12:11706868-11707332	ECC-1	luminal epithelium:	n/a	chr12:11707059-11707078
24	FOXM1	chr12:11706757-11707418	GM12878	blood:	n/a	n/a
25	YY1	chr12:11706831-11707293	GM12878	blood:	n/a	n/a
26	RAD21	chr12:11706892-11707268	HepG2	liver:	n/a	chr12:11707059-11707078
27	ESRRA	chr12:11706292-11707738	GM12878	blood:	n/a	n/a
28	RAD21	chr12:11706871-11707315	Hela-S3	cervix:	n/a	chr12:11707059-11707078
29	POLR2A	chr12:11706813-11709512	GM12878	blood:	n/a	n/a
30	CTCF	chr12:11707220-11707370	Caco-2	colon:	n/a	n/a
31	TAF1	chr12:11706967-11707364	GM12891	blood:	n/a	n/a
32	ZNF143	chr12:11706908-11707248	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr12:11706928-11707404	GM12891	blood:	n/a	n/a
34	CTCF	chr12:11706730-11707386	HCT-116	colon:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
35	EBF1	chr12:11706645-11707354	GM12878	blood:	n/a	n/a
36	REST	chr12:11706855-11707290	PFSK-1	brain:	n/a	n/a
37	TBP	chr12:11706824-11707407	GM12878	blood:	n/a	n/a
38	SMC3	chr12:11706791-11707937	SK-N-SH	brain:	n/a	chr12:11707060-11707074
39	RAD21	chr12:11706795-11707357	ECC-1	luminal epithelium:	n/a	chr12:11707059-11707078
40	CTCF	chr12:11706959-11707245	SK-N-SH_RA	brain:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
41	YY1	chr12:11706839-11707402	GM12878	blood:	n/a	n/a
42	SMC3	chr12:11706881-11707304	Hela-S3	cervix:	n/a	chr12:11707060-11707074
43	BCLAF1	chr12:11706699-11707282	GM12878	blood:	n/a	n/a
44	RAD21	chr12:11706772-11707307	HCT-116	colon:	n/a	chr12:11707059-11707078
45	RUNX3	chr12:11706810-11707374	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:11706788-11707468	GM12878	blood:	n/a	n/a
47	ZNF143	chr12:11706662-11707315	GM12878	blood:	n/a	n/a
48	POLR2A	chr12:11707068-11707346	GM12878	blood:	n/a	n/a
49	EP300	chr12:11706779-11707285	GM12878	blood:	n/a	n/a
50	CTCF	chr12:11707120-11707270	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10923458..10924277-chr12:11707052..11707592,2	K562	blood:
2	chr12:11706600..11707499-chr12:12186007..12186739,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247157	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10491980	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054355	1.00[ASN][1000 genomes]
rs11054420	1.00[EUR][1000 genomes]
rs12296206	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297330	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12304175	1.00[JPT][hapmap]
rs12306221	1.00[TSI][hapmap]
rs12306671	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12312814	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12318942	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1641623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16934824	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16935059	1.00[ASN][1000 genomes]
rs16935084	1.00[ASN][1000 genomes]
rs1795551	1.00[JPT][hapmap]
rs55959071	1.00[EUR][1000 genomes]
rs56717408	1.00[ASN][1000 genomes]
rs58160049	1.00[EUR][1000 genomes]
rs59624591	1.00[EUR][1000 genomes]
rs59692713	1.00[EUR][1000 genomes]
rs60499077	1.00[EUR][1000 genomes]
rs61366849	1.00[EUR][1000 genomes]
rs7294334	1.00[EUR][1000 genomes]
rs7305726	1.00[EUR][1000 genomes]
rs7306490	1.00[EUR][1000 genomes]
rs7308344	1.00[EUR][1000 genomes]
rs7316082	1.00[ASN][1000 genomes]
rs73286612	1.00[ASN][1000 genomes]
rs73288732	1.00[EUR][1000 genomes]
rs73288733	1.00[EUR][1000 genomes]
rs73288736	1.00[EUR][1000 genomes]
rs73288738	1.00[EUR][1000 genomes]
rs73288740	1.00[EUR][1000 genomes]
rs73288746	1.00[EUR][1000 genomes]
rs73288748	1.00[EUR][1000 genomes]
rs73288753	1.00[EUR][1000 genomes]
rs73288756	1.00[EUR][1000 genomes]
rs73288757	1.00[EUR][1000 genomes]
rs73288764	1.00[EUR][1000 genomes]
rs74060969	1.00[EUR][1000 genomes]
rs74061000	1.00[EUR][1000 genomes]
rs74062355	1.00[EUR][1000 genomes]
rs74062357	1.00[EUR][1000 genomes]
rs74062364	1.00[EUR][1000 genomes]
rs7972959	1.00[ASN][1000 genomes]
rs7975230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv469112	chr12:11575570-11711690	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv557573	chr12:11575570-11711690	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11697400-11708600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:11699000-11709000	Weak transcription	Fetal Lung	lung
3	chr12:11706400-11708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:11706600-11707400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:11706600-11708600	Enhancers	Primary T cells from cord blood	blood
6	chr12:11706800-11707400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr12:11706800-11707400	Enhancers	Primary hematopoietic stem cells	blood
8	chr12:11706800-11707400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:11706800-11707400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:11706800-11707400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:11706800-11707400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr12:11706800-11707400	Enhancers	Thymus	Thymus
13	chr12:11706800-11707600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr12:11706800-11707600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr12:11706800-11707600	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr12:11706800-11707600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr12:11706800-11707600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:11706800-11707600	Active TSS	Aorta	Aorta
19	chr12:11706800-11707600	Enhancers	Fetal Thymus	thymus
20	chr12:11706800-11707800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:11706800-11707800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:11706800-11707800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr12:11706800-11708200	Enhancers	Stomach Smooth Muscle	stomach
24	chr12:11706800-11708600	Enhancers	Colon Smooth Muscle	Colon
25	chr12:11706800-11708600	Enhancers	Rectal Smooth Muscle	rectum
26	chr12:11706800-11708800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:11706800-11708800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:11706800-11709400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr12:11706800-11709600	Enhancers	Dnd41	blood
30	chr12:11707000-11707400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:11707000-11707400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:11707200-11707400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr12:11707200-11707400	Enhancers	Brain Angular Gyrus	brain
34	chr12:11707200-11707400	Enhancers	Fetal Brain Male	brain
35	chr12:11707200-11707600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr12:11707200-11707600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr12:11707200-11707600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:11707200-11707600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr12:11707200-11707800	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr12:11707200-11707800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr12:11707200-11708000	Flanking Active TSS	GM12878-XiMat	blood
42	chr12:11707200-11708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:11707200-11708400	Weak transcription	Stomach Mucosa	stomach
44	chr12:11707200-11708600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:11707200-11708600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:11707200-11708600	Weak transcription	Rectal Mucosa Donor 31	rectum

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