Variant report

Variant	rs2063778
Chromosome Location	chr12:57811414-57811415
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57810781..57813385-chr12:57826870..57828597,2	K562	blood:
2	chr12:57811377..57813186-chr12:57823163..57825515,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179912	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000175189	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10747777	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs10747778	0.95[CEU][hapmap]
rs10783818	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs10783819	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs10876976	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876977	0.84[EUR][1000 genomes]
rs10876978	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876980	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876981	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876983	0.84[EUR][1000 genomes]
rs11172156	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs11172160	0.80[ASN][1000 genomes]
rs11172169	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172170	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap]
rs11172177	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172190	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172191	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172205	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172211	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172214	0.83[EUR][1000 genomes]
rs11172222	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11609986	0.92[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs12230111	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12296766	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs12310220	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs12369598	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12423654	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12579911	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12582640	0.86[ASN][1000 genomes]
rs12812140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1798710	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280139	0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28504983	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35032945	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3923885	0.96[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap]
rs4075325	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs4108243	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760228	0.85[EUR][1000 genomes]
rs4760236	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs4760244	0.81[EUR][1000 genomes]
rs4760305	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760306	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4760308	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4760348	0.96[CEU][hapmap];0.84[ASN][1000 genomes]
rs481196	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs491750	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs492749	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs512223	0.85[EUR][1000 genomes]
rs533975	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs537482	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs543410	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs560048	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs568793	0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs575153	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6581131	0.96[CEU][hapmap];0.87[CHB][hapmap]
rs6581134	0.85[CHB][hapmap];0.98[GIH][hapmap]
rs6581136	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7132367	0.87[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7133939	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs7135142	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs7298418	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs7303070	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7307059	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs7309659	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs7398058	0.96[CEU][hapmap];0.84[CHB][hapmap]
rs7486863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7977908	0.96[CEU][hapmap]
rs7980310	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[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	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv516655	chr12:57763520-57811414	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2063778	XRCC6BP1	cis	multi-tissue	Pritchard
rs2063778	OR6C4	cis	parietal	SCAN
rs2063778	DKFZP586D0919	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57753200-57823800	Weak transcription	Esophagus	oesophagus
2	chr12:57762800-57811800	Weak transcription	Pancreas	Pancrea
3	chr12:57766200-57816000	Weak transcription	Fetal Lung	lung
4	chr12:57770800-57824000	Weak transcription	Gastric	stomach
5	chr12:57774400-57819200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:57780800-57823200	Weak transcription	Spleen	Spleen
7	chr12:57783800-57823200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:57784200-57818000	Weak transcription	HSMM	muscle
9	chr12:57784400-57813600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:57784400-57816400	Weak transcription	NHLF	lung
11	chr12:57786400-57815600	Weak transcription	Fetal Brain Female	brain
12	chr12:57786600-57813400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:57787800-57812000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:57788600-57815200	Weak transcription	Fetal Intestine Large	intestine
15	chr12:57788600-57823200	Weak transcription	NHDF-Ad	bronchial
16	chr12:57789200-57823000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:57789400-57813400	Weak transcription	Lung	lung
18	chr12:57789400-57823200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:57789600-57815600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:57789600-57815800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr12:57789600-57816200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:57789800-57813200	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:57789800-57814400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:57789800-57814600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:57789800-57816000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:57789800-57816000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:57789800-57816200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:57790000-57813200	Weak transcription	Thymus	Thymus
29	chr12:57790000-57813600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:57790000-57814000	Weak transcription	Dnd41	blood
31	chr12:57790000-57814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:57790000-57815400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:57790000-57815800	Weak transcription	Placenta	Placenta
34	chr12:57790000-57815800	Weak transcription	GM12878-XiMat	blood
35	chr12:57790000-57816200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:57790000-57823200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:57791000-57811800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:57795400-57812000	Weak transcription	NHEK	skin
39	chr12:57795400-57813400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:57795400-57816000	Weak transcription	Brain Angular Gyrus	brain
41	chr12:57795400-57822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:57795400-57823000	Weak transcription	Brain Substantia Nigra	brain
43	chr12:57795400-57823200	Weak transcription	Adipose Nuclei	Adipose
44	chr12:57795400-57823200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:57795400-57823200	Weak transcription	HMEC	breast
46	chr12:57795400-57823600	Weak transcription	Aorta	Aorta
47	chr12:57795800-57811600	Weak transcription	Liver	Liver
48	chr12:57795800-57813000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:57795800-57823200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:57795800-57823200	Weak transcription	Right Ventricle	heart

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