Variant report

Variant	rs895957
Chromosome Location	chr12:122251656-122251657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122249312..122252163-chr12:122325172..122327877,3	K562	blood:
2	chr12:122232516..122233068-chr12:122251132..122251938,2	MCF-7	breast:
3	chr12:122248762..122251835-chr12:122331420..122334118,3	MCF-7	breast:
4	chr12:122250365..122256158-chr12:122324216..122328328,5	MCF-7	breast:
5	chr12:122247695..122252163-chr12:122325172..122328033,7	K562	blood:
6	chr12:122248283..122252969-chr12:122325592..122328736,7	MCF-7	breast:
7	chr12:122220378..122221895-chr12:122249646..122252036,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000110801	Chromatin interaction
ENSG00000256950	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1004390	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11043202	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043207	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1168663	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168664	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168665	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168666	1.00[CEU][hapmap];0.80[GIH][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168668	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168669	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168671	1.00[CEU][hapmap];0.80[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1168672	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168673	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12307227	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313997	0.89[ASN][1000 genomes]
rs12314801	0.89[ASN][1000 genomes]
rs12820413	0.82[ASN][1000 genomes]
rs12823194	0.87[EUR][1000 genomes]
rs1667578	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1667579	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1795965	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795966	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2019561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019562	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2122266	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2707057	0.82[ASN][1000 genomes]
rs2707066	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2707067	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712852	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7957564	0.94[EUR][1000 genomes]
rs7974348	1.00[CEU][hapmap];0.80[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs895951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895952	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895954	1.00[CEU][hapmap];0.80[GIH][hapmap];0.80[LWK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs921286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921288	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs930665	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
5	nsv911	chr12:122234524-122279425	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs895957	LOC338799	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122247800-122252000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:122249400-122252000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr12:122250200-122251800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr12:122250400-122252000	Enhancers	Fetal Heart	heart
5	chr12:122250600-122251800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:122250600-122251800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:122250600-122251800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:122250600-122252000	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr12:122250600-122253200	Genic enhancers	Spleen	Spleen
10	chr12:122250800-122251800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:122250800-122251800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:122250800-122251800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:122250800-122251800	Genic enhancers	Lung	lung
14	chr12:122250800-122252000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:122250800-122252000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:122250800-122252000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:122250800-122252000	Genic enhancers	Dnd41	blood
18	chr12:122250800-122252200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:122250800-122252800	Genic enhancers	Placenta	Placenta
20	chr12:122250800-122253400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr12:122250800-122254800	Weak transcription	Psoas Muscle	Psoas
22	chr12:122250800-122270200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:122250800-122270400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:122250800-122277200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:122251000-122251800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:122251000-122251800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:122251000-122251800	Enhancers	Colon Smooth Muscle	Colon
28	chr12:122251000-122251800	Enhancers	Left Ventricle	heart
29	chr12:122251000-122251800	Genic enhancers	A549	lung
30	chr12:122251000-122251800	Genic enhancers	HMEC	breast
31	chr12:122251000-122252000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:122251000-122252000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:122251000-122252000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr12:122251000-122252000	Genic enhancers	Liver	Liver
35	chr12:122251000-122252000	Genic enhancers	Brain Cingulate Gyrus	brain
36	chr12:122251000-122252000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
37	chr12:122251000-122252000	Enhancers	Stomach Mucosa	stomach
38	chr12:122251000-122252000	Genic enhancers	NHEK	skin
39	chr12:122251000-122254400	Genic enhancers	Thymus	Thymus
40	chr12:122251000-122270200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:122251000-122270400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:122251200-122251800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr12:122251200-122251800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:122251200-122251800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
45	chr12:122251200-122251800	Weak transcription	Fetal Brain Male	brain
46	chr12:122251200-122251800	Genic enhancers	Fetal Intestine Large	intestine
47	chr12:122251200-122251800	Enhancers	Pancreas	Pancrea
48	chr12:122251200-122251800	Genic enhancers	HepG2	liver
49	chr12:122251200-122252000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr12:122251200-122252000	Genic enhancers	Brain Hippocampus Middle	brain

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