Variant report

Variant	rs1805667
Chromosome Location	chr12:9219966-9219967
allele	G/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	chr12:9216895-9230988	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:9216806-9219983	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:9216389-9221070	HepG2	liver:	n/a	n/a
4	MYBL2	chr12:9218472-9220191	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:9217415-9220251	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:9216589-9220417	HepG2	liver:	n/a	n/a
7	MBD4	chr12:9218464-9220244	HepG2	liver:	n/a	n/a
8	NFIC	chr12:9218583-9220189	HepG2	liver:	n/a	n/a
9	STAT3	chr12:9219656-9220014	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr12:9216161-9220988	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9218102..9220634-chr12:9230847..9232385,2	MCF-7	breast:
2	chr12:9218454..9221005-chr12:9232709..9234704,2	K562	blood:

Variant related genes	Relation type
LINC00612	TF binding region
ENSG00000175899	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10771307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842820	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842845	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842898	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[EUR][1000 genomes]
rs11048789	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805651	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805652	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805653	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805654	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805655	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805656	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805657	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805658	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805659	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805660	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1805663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1805664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805666	0.90[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805678	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805681	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2193005	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs226379	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes]
rs226383	0.94[EUR][1000 genomes]
rs226384	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes]
rs226393	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs226395	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[EUR][1000 genomes]
rs2300147	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300148	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2377682	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487574	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487581	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487585	0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487587	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7135781	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7299282	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7299600	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7309361	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310089	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310167	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310884	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310921	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965184	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968640	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7976461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs881376	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription 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	38 gene(s)	inside rSNPs	diseases
3	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS 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	9 gene(s)	inside rSNPs	diseases
4	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9217400-9223400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:9217600-9223200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:9217800-9220400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:9217800-9225000	Weak transcription	Small Intestine	intestine
5	chr12:9217800-9234200	Weak transcription	Primary T cells from cord blood	blood
6	chr12:9218000-9220000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:9218000-9226800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:9218000-9234000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:9218200-9220000	Enhancers	Hela-S3	cervix
10	chr12:9218200-9220000	Enhancers	HMEC	breast
11	chr12:9218200-9223000	Weak transcription	Aorta	Aorta
12	chr12:9218200-9223200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:9218200-9224200	Weak transcription	Ovary	ovary
14	chr12:9218200-9232200	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:9218200-9236200	Weak transcription	Psoas Muscle	Psoas
16	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
17	chr12:9218400-9220000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:9218400-9220200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:9218400-9220200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:9218400-9220400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:9218400-9223800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr12:9218400-9224200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:9218400-9224200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:9218400-9224600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:9218400-9228600	Weak transcription	Brain Anterior Caudate	brain
26	chr12:9218400-9230800	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:9218400-9231000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr12:9218400-9234400	Weak transcription	Right Atrium	heart
29	chr12:9218400-9236600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:9218400-9236600	Weak transcription	Brain Substantia Nigra	brain
31	chr12:9218400-9237200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:9218600-9220400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:9218600-9220600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:9218600-9225000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:9218600-9229400	Weak transcription	Colonic Mucosa	Colon
36	chr12:9218600-9235600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:9218600-9235800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:9218600-9236400	Weak transcription	Brain Angular Gyrus	brain
39	chr12:9218800-9220800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:9218800-9225000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr12:9218800-9230400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:9218800-9236200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:9218800-9236200	Weak transcription	Fetal Heart	heart
44	chr12:9219000-9220000	Enhancers	Fetal Intestine Small	intestine
45	chr12:9219000-9220000	Enhancers	HepG2	liver
46	chr12:9219000-9220200	Weak transcription	Left Ventricle	heart
47	chr12:9219000-9220600	Weak transcription	Placenta	Placenta
48	chr12:9219000-9223000	Weak transcription	Spleen	Spleen
49	chr12:9219000-9224000	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:9219000-9233200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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