Variant report

Variant	rs2286040
Chromosome Location	chr12:120502726-120502727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120502380..120507163-chr12:120508034..120511527,6	K562	blood:
2	chr12:120502350..120506477-chr12:120508342..120509946,3	K562	blood:
3	chr12:120500334..120503561-chr12:120515815..120519326,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135127	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10128766	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10400498	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][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]
rs10400560	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849731	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10849732	0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10849735	0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs10849736	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11064987	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11064988	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11064996	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11833221	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12310269	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12310591	0.97[ASN][1000 genomes]
rs12313413	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12318774	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12320793	0.90[ASN][1000 genomes]
rs12322236	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422923	0.97[ASN][1000 genomes]
rs16949901	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16949946	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16949961	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17841967	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239200	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239201	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239202	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2239203	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239204	0.94[ASN][1000 genomes]
rs2240311	0.82[CHB][hapmap]
rs2283359	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283360	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28726166	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3742042	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4105713	0.82[ASN][1000 genomes]
rs4767869	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4767871	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767872	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767875	0.97[ASN][1000 genomes]
rs4767876	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]
rs58272825	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59168361	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60466490	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6490281	0.91[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs7298183	0.91[ASN][1000 genomes]
rs7298727	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7300023	0.86[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7312971	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7314959	0.83[CHB][hapmap]
rs7397339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7956436	0.82[CHB][hapmap]
rs7958402	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7958497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7965829	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7968557	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7978927	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120486800-120512000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:120487800-120512200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:120493000-120503200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:120493800-120523800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:120494800-120517800	Weak transcription	Lung	lung
6	chr12:120497600-120502800	Enhancers	Hela-S3	cervix
7	chr12:120497600-120507400	Enhancers	Stomach Mucosa	stomach
8	chr12:120497600-120509400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr12:120498200-120507400	Strong transcription	Primary T cells from cord blood	blood
10	chr12:120498400-120511600	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:120498600-120503600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:120498600-120504200	Enhancers	Brain Angular Gyrus	brain
13	chr12:120498800-120516600	Weak transcription	Fetal Brain Male	brain
14	chr12:120499200-120504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:120499200-120506000	Strong transcription	Thymus	Thymus
16	chr12:120499200-120507800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:120499400-120503600	Enhancers	HepG2	liver
18	chr12:120499400-120505400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:120499400-120506400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:120499400-120509400	Weak transcription	Pancreas	Pancrea
21	chr12:120499800-120511200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr12:120499800-120516400	Weak transcription	Primary B cells from cord blood	blood
23	chr12:120500200-120502800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:120500200-120503600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:120500400-120503000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:120501000-120504800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:120501200-120502800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:120501200-120502800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:120501600-120502800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr12:120501600-120502800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:120501600-120502800	Enhancers	Fetal Heart	heart
32	chr12:120501600-120503000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:120501600-120503800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr12:120501800-120503000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:120502000-120502800	Enhancers	Placenta Amnion	Placenta Amnion
36	chr12:120502000-120506600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:120502000-120523400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr12:120502200-120503200	Weak transcription	Brain Substantia Nigra	brain
39	chr12:120502200-120503600	Enhancers	Brain Cingulate Gyrus	brain
40	chr12:120502200-120505800	Weak transcription	Right Ventricle	heart
41	chr12:120502200-120509600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr12:120502200-120509600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:120502200-120516600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr12:120502200-120517800	Weak transcription	Gastric	stomach
45	chr12:120502400-120503400	Strong transcription	Fetal Thymus	thymus
46	chr12:120502400-120503600	Enhancers	Brain Hippocampus Middle	brain
47	chr12:120502400-120503600	Strong transcription	Esophagus	oesophagus
48	chr12:120502400-120503600	Strong transcription	Fetal Brain Female	brain
49	chr12:120502400-120503800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:120502400-120504200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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