Variant report

Variant	rs2012937
Chromosome Location	chr12:45674461-45674462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:45625441..45631111-chr12:45668814..45675582,6	MCF-7	breast:
2	chr12:45672681..45674685-chr12:45684107..45686639,2	MCF-7	breast:
3	chr12:45622554..45624408-chr12:45673462..45676280,2	K562	blood:

Variant related genes	Relation type
ENSG00000177119	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1015625	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1015626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1025088	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10459295	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs10467095	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10736024	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs10748412	0.83[ASN][1000 genomes]
rs10748416	0.98[AFR][1000 genomes]
rs10785564	0.92[YRI][hapmap];1.00[AFR][1000 genomes]
rs10785566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10785569	0.90[TSI][hapmap]
rs10880761	0.86[JPT][hapmap]
rs10880762	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10880764	0.82[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap]
rs10880765	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs10880766	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs10880768	0.89[EUR][1000 genomes]
rs10880771	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182905	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs11182918	0.86[JPT][hapmap]
rs11182949	0.82[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs11182954	0.82[CEU][hapmap]
rs11182955	0.82[CEU][hapmap]
rs11182957	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs11182961	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs11182965	0.82[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11182966	0.89[EUR][1000 genomes]
rs11182969	0.89[EUR][1000 genomes]
rs11182970	0.89[EUR][1000 genomes]
rs11182973	0.84[EUR][1000 genomes]
rs11182974	0.84[EUR][1000 genomes]
rs11182981	0.82[CEU][hapmap]
rs11182986	0.90[TSI][hapmap]
rs11182988	0.90[TSI][hapmap]
rs11183014	0.89[TSI][hapmap]
rs11183029	0.90[TSI][hapmap]
rs11614082	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11614089	0.89[EUR][1000 genomes]
rs12228399	0.89[EUR][1000 genomes]
rs12230322	0.86[JPT][hapmap]
rs12231753	0.86[JPT][hapmap]
rs12297071	0.90[TSI][hapmap]
rs12320168	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs12815577	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1399721	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863549	0.90[TSI][hapmap]
rs1896027	0.82[ASW][hapmap]
rs1913690	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1913692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2037856	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2037857	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2052603	0.82[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs2408184	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs34759896	0.89[EUR][1000 genomes]
rs35032811	0.89[EUR][1000 genomes]
rs35400022	0.84[EUR][1000 genomes]
rs3803178	0.90[TSI][hapmap]
rs4326862	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768085	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs4768598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768600	0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs4768601	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4768602	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4768603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582541	0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136281	1.00[ASW][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7136368	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7138247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs728590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7304389	0.82[ASW][hapmap]
rs7304481	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs7307262	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309615	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7310046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487910	0.83[ASN][1000 genomes]
rs7965430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7970250	0.82[ASW][hapmap]

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	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
2	nsv690	chr12:45674127-45718859	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45651400-45675600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:45654400-45725600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:45662800-45677400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:45662800-45685400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:45662800-45696800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr12:45663000-45677400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:45663000-45677600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:45663000-45678200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:45663200-45678400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:45663400-45677400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:45663400-45677400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:45663400-45680400	Weak transcription	GM12878-XiMat	blood
13	chr12:45663600-45677000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:45664000-45676000	Weak transcription	Fetal Stomach	stomach
15	chr12:45664000-45678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:45664400-45677600	Weak transcription	Fetal Kidney	kidney
17	chr12:45665600-45676000	Weak transcription	Thymus	Thymus
18	chr12:45666200-45709200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:45668000-45677400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:45668200-45676000	Weak transcription	Gastric	stomach
21	chr12:45668200-45677400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:45668200-45678200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:45668400-45675400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:45668400-45697800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:45668600-45677400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:45668600-45677600	Weak transcription	Spleen	Spleen
27	chr12:45668600-45679200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:45668600-45693000	Weak transcription	Pancreas	Pancrea
29	chr12:45668800-45675000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:45668800-45675200	Weak transcription	Lung	lung
31	chr12:45668800-45675600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:45668800-45676600	Weak transcription	HUVEC	blood vessel
33	chr12:45668800-45677000	Weak transcription	HMEC	breast
34	chr12:45668800-45677200	Weak transcription	HSMM	muscle
35	chr12:45668800-45677200	Weak transcription	NH-A	brain
36	chr12:45668800-45677200	Weak transcription	NHDF-Ad	bronchial
37	chr12:45668800-45677400	Weak transcription	Hela-S3	cervix
38	chr12:45670200-45675200	Weak transcription	NHEK	skin
39	chr12:45670200-45677200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:45670200-45677400	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:45670200-45677600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:45670200-45677800	Weak transcription	HSMMtube	muscle
43	chr12:45670200-45680600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:45670400-45675600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:45670400-45675600	Weak transcription	Esophagus	oesophagus
46	chr12:45670400-45676400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:45670400-45677000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:45670400-45677600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr12:45670600-45675200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:45670800-45677600	Weak transcription	NHLF	lung

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