Variant report

Variant	rs2035081
Chromosome Location	chr12:57125879-57125880
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	E2F4	chr12:57125766-57125908	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57117403..57120848-chr12:57123897..57127833,5	MCF-7	breast:
2	chr12:57124041..57126184-chr12:57145375..57147304,2	MCF-7	breast:
3	chr12:57117154..57122230-chr12:57122473..57127950,8	K562	blood:

Variant related genes	Relation type
NACA	TF binding region
ENSG00000196531	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000025423	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1026565	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10450	0.80[CHB][hapmap]
rs10459246	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747769	0.82[EUR][1000 genomes]
rs10747770	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783794	0.81[CHB][hapmap]
rs10783796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876916	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10876918	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107479	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs11171914	0.90[CEU][hapmap];0.84[CHB][hapmap]
rs11171951	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171956	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171986	0.81[JPT][hapmap]
rs1131514	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12227117	0.82[ASN][1000 genomes]
rs12229457	0.90[CEU][hapmap];0.87[CHB][hapmap]
rs12828563	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1466382	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563896	0.85[CEU][hapmap];0.80[CHB][hapmap];0.83[ASN][1000 genomes]
rs1563897	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1975875	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1979325	0.93[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2035082	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255074	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap]
rs2290893	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2290894	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926741	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2926743	0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2926747	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2926748	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950387	0.86[TSI][hapmap]
rs2950390	0.90[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs2958123	0.95[CEU][hapmap];0.87[CHB][hapmap]
rs2958127	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958130	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958132	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958134	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2958148	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2958149	0.87[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2958153	0.87[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2958154	0.90[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs2958155	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs3214051	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4277148	0.81[JPT][hapmap]
rs4759254	0.82[CEU][hapmap]
rs4759256	0.90[ASN][1000 genomes]
rs4788	0.96[ASN][1000 genomes]
rs4902	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137749	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7295862	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7297289	0.80[ASN][1000 genomes]
rs7303216	0.80[ASN][1000 genomes]
rs7313074	0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7966391	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978685	0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7980317	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7980835	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs898609	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898611	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9634246	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs9989034	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1794914	chr12:57119236-57195379	Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2035081	HSD17B6	cis	cerebellum	SCAN
rs2035081	RAB5B	cis	cerebellum	SCAN
rs2035081	OR6C4	cis	cerebellum	SCAN
rs2035081	CELA1	cis	cerebellum	SCAN
rs2035081	MUCL1	cis	parietal	SCAN
rs2035081	PRIM1	cis	cerebellum	SCAN
rs2035081	PRIM1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57119200-57127400	Weak transcription	Spleen	Spleen
2	chr12:57119200-57130400	Weak transcription	Gastric	stomach
3	chr12:57119400-57129000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:57119400-57130600	Weak transcription	Small Intestine	intestine
5	chr12:57119400-57134000	Weak transcription	Esophagus	oesophagus
6	chr12:57119400-57138000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:57119400-57145000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:57119600-57128800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:57119600-57129000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:57119600-57130600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:57119600-57130600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:57119600-57130600	Weak transcription	Lung	lung
13	chr12:57119600-57130600	Weak transcription	Pancreas	Pancrea
14	chr12:57119800-57128800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:57119800-57130400	Weak transcription	Ovary	ovary
16	chr12:57119800-57131800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:57119800-57134000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:57119800-57134000	Weak transcription	Left Ventricle	heart
19	chr12:57119800-57144600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:57119800-57144800	Weak transcription	NHLF	lung
21	chr12:57119800-57145000	Weak transcription	Colonic Mucosa	Colon
22	chr12:57119800-57145000	Weak transcription	Right Ventricle	heart
23	chr12:57120000-57126200	Weak transcription	HMEC	breast
24	chr12:57120000-57127600	Weak transcription	Fetal Lung	lung
25	chr12:57120000-57128200	Weak transcription	Thymus	Thymus
26	chr12:57120000-57129200	Weak transcription	Fetal Intestine Large	intestine
27	chr12:57120000-57130400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:57120000-57130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:57120000-57130400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:57120000-57130600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:57120000-57130600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:57120000-57130800	Weak transcription	Placenta	Placenta
33	chr12:57120000-57130800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:57120000-57131600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:57120000-57131600	Weak transcription	Brain Substantia Nigra	brain
36	chr12:57120000-57133200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:57120000-57134200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:57120000-57134200	Weak transcription	Brain Angular Gyrus	brain
39	chr12:57120000-57134800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:57120000-57137200	Weak transcription	NHEK	skin
41	chr12:57120000-57138400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr12:57120000-57140400	Weak transcription	HUVEC	blood vessel
43	chr12:57120000-57144400	Weak transcription	Fetal Brain Male	brain
44	chr12:57120000-57144600	Weak transcription	NHDF-Ad	bronchial
45	chr12:57120000-57144800	Weak transcription	Fetal Heart	heart
46	chr12:57120000-57144800	Weak transcription	Fetal Kidney	kidney
47	chr12:57120000-57144800	Weak transcription	NH-A	brain
48	chr12:57120000-57145000	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:57120000-57145200	Weak transcription	Aorta	Aorta
50	chr12:57120200-57127600	Weak transcription	Stomach Smooth Muscle	stomach

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