Variant report

Variant	rs12612557
Chromosome Location	chr2:152995261-152995262
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	chr2:152991291..152993759-chr2:152994536..152996145,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10177222	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10187630	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10203659	0.82[ASW][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap]
rs10469642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10497095	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10497097	0.87[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10803946	0.84[CEU][hapmap];0.90[TSI][hapmap]
rs10930923	0.85[GIH][hapmap];0.85[MEX][hapmap]
rs10930939	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930959	0.89[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1133478	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11694120	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11884659	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11893841	0.89[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12328733	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12468532	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12472524	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12476550	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12613984	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615156	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621378	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622092	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12623355	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12693270	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12693271	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13003423	0.89[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13424583	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2002247	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28785043	0.82[AMR][1000 genomes]
rs34233450	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35155943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35717822	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3768648	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768649	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768651	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806464	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4255959	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4368329	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4473376	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4505521	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4611639	0.86[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4664080	0.86[ASN][1000 genomes]
rs4664084	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664085	0.89[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4664089	0.84[CEU][hapmap];0.84[LWK][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap]
rs4664530	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664531	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4664532	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4664535	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664537	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62176474	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62176476	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62176478	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62176479	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6650779	0.88[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6720552	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71417204	0.86[ASN][1000 genomes]
rs7420277	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7572616	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7588906	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8179814	0.81[AMR][1000 genomes]
rs9917198	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv3693432	chr2:152986041-152997726	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv459740	chr2:152986041-153045036	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv583316	chr2:152986041-153045036	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12612557	STAM2	cis	parietal	SCAN
rs12612557	STAM2	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152968000-152995800	Weak transcription	HSMMtube	muscle
2	chr2:152970200-153003000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:152971200-153008400	Weak transcription	Esophagus	oesophagus
4	chr2:152971400-153002200	Weak transcription	Brain Anterior Caudate	brain
5	chr2:152974200-153001400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:152974200-153017000	Weak transcription	Colonic Mucosa	Colon
7	chr2:152974800-153002000	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:152974800-153003800	Weak transcription	NHEK	skin
9	chr2:152974800-153008200	Weak transcription	Fetal Brain Female	brain
10	chr2:152975000-153003200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:152975000-153003600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:152975000-153005400	Weak transcription	Brain Germinal Matrix	brain
13	chr2:152976000-153014800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:152976200-153010200	Weak transcription	Fetal Brain Male	brain
15	chr2:152976200-153013400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:152976400-153005000	Weak transcription	Fetal Heart	heart
17	chr2:152976400-153013400	Weak transcription	Brain Angular Gyrus	brain
18	chr2:152976800-153003000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:152977400-153006200	Weak transcription	HMEC	breast
20	chr2:152978000-153001600	Weak transcription	Lung	lung
21	chr2:152978200-153000000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:152978200-153021400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:152978400-153003400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:152979000-153001400	Weak transcription	Small Intestine	intestine
25	chr2:152979000-153002000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:152979400-153001400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:152979600-152997400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:152979600-152999000	Weak transcription	Fetal Thymus	thymus
29	chr2:152979600-152999600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:152979600-153001600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:152980200-153001200	Weak transcription	Aorta	Aorta
32	chr2:152980200-153001200	Weak transcription	Spleen	Spleen
33	chr2:152980400-152997000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:152980400-153001200	Weak transcription	Pancreas	Pancrea
35	chr2:152981400-152996800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:152981800-153024800	Weak transcription	Brain Substantia Nigra	brain
37	chr2:152982200-152996600	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:152982200-152998400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:152982200-152998400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr2:152982200-152998600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:152982200-153001200	Weak transcription	Ovary	ovary
42	chr2:152982200-153001200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:152982200-153001200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:152982400-152995400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr2:152982400-152998600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:152982400-153013400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:152983800-153013400	Weak transcription	Psoas Muscle	Psoas
48	chr2:152986000-153001600	Weak transcription	Left Ventricle	heart
49	chr2:152986200-152996000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:152986400-152999400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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