Variant report

Variant	rs11585888
Chromosome Location	chr1:62499673-62499674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10493313	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11576777	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577828	1.00[JPT][hapmap]
rs11579010	0.95[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11581307	1.00[JPT][hapmap]
rs11587128	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11590485	1.00[JPT][hapmap]
rs11590812	1.00[JPT][hapmap]
rs11590954	1.00[JPT][hapmap]
rs1332631	0.85[JPT][hapmap]
rs1412620	0.82[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17313395	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17378995	0.95[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs2067881	1.00[JPT][hapmap]
rs2476180	1.00[JPT][hapmap]
rs4325166	1.00[JPT][hapmap]
rs56379320	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61777663	0.92[ASN][1000 genomes]
rs61777664	0.92[ASN][1000 genomes]
rs6661849	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673889	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682776	0.92[MEX][hapmap]
rs6685356	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685442	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519802	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528431	1.00[JPT][hapmap]
rs7531027	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7539653	0.80[ASW][hapmap];0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547886	0.86[CEU][hapmap]
rs7556298	0.83[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	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11585888	TACSTD2	cis	cerebellum	SCAN
rs11585888	NFIA	cis	cerebellum	SCAN
rs11585888	DAB1	cis	parietal	SCAN
rs11585888	RAVER2	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
2	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:62459000-62516000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:62459200-62511200	Weak transcription	Gastric	stomach
6	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:62460000-62516400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:62460200-62516000	Weak transcription	HMEC	breast
10	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:62474200-62518600	Weak transcription	Primary T cells from cord blood	blood
12	chr1:62480600-62513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:62484400-62523000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:62484600-62506000	Weak transcription	NHEK	skin
16	chr1:62484800-62511200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:62486200-62517600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:62488400-62521200	Weak transcription	Ovary	ovary
19	chr1:62491800-62511200	Weak transcription	Psoas Muscle	Psoas
20	chr1:62494600-62504600	Weak transcription	Aorta	Aorta
21	chr1:62494600-62511200	Weak transcription	Fetal Intestine Small	intestine
22	chr1:62494600-62524400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:62494600-62524400	Weak transcription	Esophagus	oesophagus
24	chr1:62494800-62505200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:62495000-62504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:62495000-62515200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:62495200-62516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:62495200-62544800	Weak transcription	Liver	Liver
29	chr1:62496200-62504600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:62496600-62500400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr1:62497200-62515000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:62497400-62500000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr1:62497600-62500200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:62497800-62500400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:62498400-62500400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr1:62498600-62500600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:62499000-62499800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:62499000-62500000	Enhancers	H9 Cell Line	embryonic stem cell
39	chr1:62499000-62500000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:62499000-62500000	Enhancers	Fetal Heart	heart
41	chr1:62499200-62500000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:62499200-62500400	Enhancers	Right Ventricle	heart
43	chr1:62499400-62499800	Weak transcription	Left Ventricle	heart
44	chr1:62499400-62499800	Weak transcription	Right Atrium	heart
45	chr1:62499400-62500800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr1:62499400-62501400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:62499400-62504200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:62499600-62500000	Strong transcription	Fetal Intestine Large	intestine
49	chr1:62499600-62501600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:62499600-62502000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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