Variant report

Variant	rs11111751
Chromosome Location	chr12:104155714-104155715
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	chr12:104155678-104155818	K562	blood:	n/a	n/a

Variant related genes	Relation type
STAB2	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10735389	0.81[CHD][hapmap]
rs10778285	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861092	0.81[AMR][1000 genomes]
rs10861093	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861098	1.00[ASN][1000 genomes]
rs10861099	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10861102	0.89[ASN][1000 genomes]
rs10861103	1.00[ASN][1000 genomes]
rs11111761	0.81[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111764	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111766	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111772	1.00[ASN][1000 genomes]
rs11111773	1.00[ASN][1000 genomes]
rs11111775	1.00[ASN][1000 genomes]
rs11111781	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11111782	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11111783	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs11111787	0.99[ASN][1000 genomes]
rs12424737	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs12425205	0.84[CHD][hapmap]
rs1370777	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1370778	0.97[ASN][1000 genomes]
rs1370779	1.00[ASN][1000 genomes]
rs1866293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1866294	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1866296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1968513	1.00[ASN][1000 genomes]
rs2888792	1.00[ASN][1000 genomes]
rs3751205	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812804	0.85[CHD][hapmap]
rs4964813	0.99[ASN][1000 genomes]
rs4964814	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4964819	0.97[ASN][1000 genomes]
rs4964820	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4981034	0.81[CHD][hapmap]
rs4981035	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5001722	1.00[ASN][1000 genomes]
rs61602054	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6539101	0.85[CHD][hapmap]
rs7136682	0.91[ASN][1000 genomes]
rs7296900	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7312606	0.99[ASN][1000 genomes]
rs7312825	0.99[ASN][1000 genomes]
rs73192049	0.96[ASN][1000 genomes]
rs7970553	0.85[CHD][hapmap]
rs7973081	1.00[ASN][1000 genomes]
rs9084	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9142	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934843	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs934845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs934846	0.97[ASN][1000 genomes]
rs954921	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs9706225	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899486	chr12:104118587-104170474	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv899491	chr12:104151560-104175575	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11111751	TU12B1-TY	cis	multi-tissue	Pritchard
rs11111751	ACTR6	cis	parietal	SCAN
rs11111751	RP11-341G23.4	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104145800-104166800	Weak transcription	Right Atrium	heart
2	chr12:104146200-104169400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:104147000-104159600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:104147000-104165400	Strong transcription	Stomach Smooth Muscle	stomach
5	chr12:104147400-104155800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:104149000-104156800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:104150000-104156600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:104150000-104166800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:104151400-104158000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:104151600-104170400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:104152000-104159800	Weak transcription	Lung	lung
12	chr12:104152400-104159400	Weak transcription	Gastric	stomach
13	chr12:104152400-104160000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:104152400-104162600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:104152400-104162800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:104152600-104158600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:104152600-104160600	Strong transcription	Spleen	Spleen
18	chr12:104152600-104161600	Strong transcription	HMEC	breast
19	chr12:104152600-104162600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:104152600-104162600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:104152600-104162800	Weak transcription	Psoas Muscle	Psoas
22	chr12:104152600-104171200	Weak transcription	Esophagus	oesophagus
23	chr12:104152800-104156200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:104152800-104159000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:104152800-104159200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:104152800-104159600	Weak transcription	Fetal Muscle Leg	muscle
27	chr12:104152800-104162800	Weak transcription	Brain Angular Gyrus	brain
28	chr12:104152800-104165400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:104153000-104155800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:104153000-104156200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:104153200-104162800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:104153400-104156000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:104153800-104161600	Strong transcription	Liver	Liver
35	chr12:104154200-104157200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:104154200-104157600	Strong transcription	Rectal Smooth Muscle	rectum
37	chr12:104154200-104158400	Strong transcription	Placenta	Placenta
38	chr12:104154200-104161800	Strong transcription	Colon Smooth Muscle	Colon
39	chr12:104154400-104157600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:104154400-104159600	Weak transcription	Fetal Intestine Large	intestine
41	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:104154600-104156200	Weak transcription	Pancreas	Pancrea
43	chr12:104154600-104157600	Strong transcription	HSMM	muscle
44	chr12:104154600-104158200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:104154600-104160400	Strong transcription	NHEK	skin
46	chr12:104154600-104160600	Strong transcription	Aorta	Aorta
47	chr12:104154600-104160600	Strong transcription	Fetal Stomach	stomach
48	chr12:104154800-104157400	Strong transcription	HSMMtube	muscle
49	chr12:104154800-104157600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:104154800-104161400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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