Variant report

Variant	rs4664085
Chromosome Location	chr2:153023750-153023751
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153023103..153025795-chr2:153030743..153032698,4	K562	blood:
2	chr2:153023722..153029811-chr2:153030516..153033804,9	MCF-7	breast:
3	chr2:153021796..153023898-chr2:153029429..153032358,3	K562	blood:

Variant related genes	Relation type
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10177222	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10187630	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10203659	0.90[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs10469642	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10497095	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10497097	1.00[ASW][hapmap];0.90[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10803946	0.95[CEU][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10930923	0.90[GIH][hapmap];1.00[MEX][hapmap]
rs10930939	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10930959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10930967	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1133478	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11679305	0.82[EUR][1000 genomes]
rs11694120	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11884659	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11893841	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12328733	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12468532	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12472524	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12476550	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12612557	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]
rs12613984	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12615156	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621378	0.85[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12622092	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12623355	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12693270	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12693271	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12693296	0.83[EUR][1000 genomes]
rs13003423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13424583	0.88[EUR][1000 genomes]
rs2002247	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28396364	0.81[EUR][1000 genomes]
rs28785043	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34233450	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34657619	0.81[EUR][1000 genomes]
rs35155943	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35717822	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3768648	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3768649	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3768651	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806464	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4255959	0.86[EUR][1000 genomes]
rs4368329	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4473376	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4505521	0.86[EUR][1000 genomes]
rs4611639	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4664080	0.81[ASN][1000 genomes]
rs4664084	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664089	0.95[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs4664530	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4664531	0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4664532	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4664535	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4664537	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62176474	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62176476	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62176478	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62176479	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6650779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6720552	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs71417204	0.84[ASN][1000 genomes]
rs7420277	0.83[EUR][1000 genomes]
rs7572616	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7588906	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8179814	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9917198	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	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
10	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
11	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	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
rs4664085	STAM2	cis	parietal	SCAN
rs4664085	STAM2	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152981800-153024800	Weak transcription	Brain Substantia Nigra	brain
2	chr2:153000200-153031000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:153002800-153030400	Weak transcription	Thymus	Thymus
4	chr2:153003200-153028400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:153003600-153028000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:153004200-153023800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:153005200-153028000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:153005200-153028200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:153007200-153028200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:153008800-153028800	Weak transcription	Esophagus	oesophagus
11	chr2:153014000-153028400	Weak transcription	Right Ventricle	heart
12	chr2:153014200-153023800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:153014200-153023800	Weak transcription	Brain Anterior Caudate	brain
14	chr2:153014200-153024000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:153014200-153028400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:153014200-153028400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:153015400-153030200	Weak transcription	Primary T cells from cord blood	blood
18	chr2:153017000-153030200	Weak transcription	Fetal Stomach	stomach
19	chr2:153021200-153030600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:153021400-153025000	Enhancers	Ovary	ovary
21	chr2:153021400-153028200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:153021800-153024200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr2:153022000-153024000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:153022000-153024400	Enhancers	Small Intestine	intestine
25	chr2:153022200-153024400	Enhancers	Liver	Liver
26	chr2:153022200-153031400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:153022400-153024000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:153022400-153024000	Enhancers	Colon Smooth Muscle	Colon
29	chr2:153022400-153024000	Enhancers	Rectal Smooth Muscle	rectum
30	chr2:153022400-153024200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr2:153022400-153024200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:153022400-153024200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:153022600-153023800	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr2:153022600-153023800	Weak transcription	Fetal Intestine Small	intestine
35	chr2:153022600-153024000	Enhancers	Primary B cells from peripheral blood	blood
36	chr2:153022600-153024000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr2:153022600-153024000	Enhancers	K562	blood
38	chr2:153022600-153025400	Enhancers	A549	lung
39	chr2:153022600-153028600	Weak transcription	Right Atrium	heart
40	chr2:153022600-153028800	Weak transcription	Spleen	Spleen
41	chr2:153022800-153023800	Weak transcription	Psoas Muscle	Psoas
42	chr2:153022800-153024000	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr2:153022800-153024000	Enhancers	NH-A	brain
44	chr2:153022800-153025800	Weak transcription	Lung	lung
45	chr2:153022800-153025800	Weak transcription	Pancreas	Pancrea
46	chr2:153022800-153026200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:153022800-153028400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr2:153022800-153031200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:153022800-153031200	Weak transcription	Gastric	stomach
50	chr2:153022800-153031200	Weak transcription	Left Ventricle	heart

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