Variant report

Variant	rs7588227
Chromosome Location	chr2:98562116-98562117
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:98560562..98563114-chr2:98618260..98620313,2	K562	blood:
2	chr2:98560596..98562974-chr2:98563175..98565676,2	MCF-7	breast:
3	chr2:98561365..98564019-chr2:98567762..98570732,2	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10166513	0.94[ASN][1000 genomes]
rs10167772	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10168543	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10168709	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10175129	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10176826	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10180434	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180837	0.80[EUR][1000 genomes]
rs10183768	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10184457	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10184552	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10188497	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10188713	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10189414	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191101	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10191483	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10192322	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap]
rs10202138	0.94[ASN][1000 genomes]
rs10206684	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10208070	0.84[EUR][1000 genomes]
rs10209970	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10210299	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10210520	0.88[ASN][1000 genomes]
rs10210880	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024086	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11886417	1.00[ASN][1000 genomes]
rs11893437	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11894541	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11894895	0.88[ASN][1000 genomes]
rs11895170	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11897301	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712117	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712120	0.88[ASN][1000 genomes]
rs12712147	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12712162	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712163	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712172	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12992955	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13000585	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13008678	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13008904	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13010004	0.88[ASN][1000 genomes]
rs13012645	0.83[EUR][1000 genomes]
rs13387725	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13404788	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13427422	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1446327	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1503202	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1960329	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1982336	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs2121271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2293679	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs2305142	0.81[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs34190123	0.94[ASN][1000 genomes]
rs34305873	0.80[AMR][1000 genomes]
rs34414288	0.88[ASN][1000 genomes]
rs34469351	0.97[ASN][1000 genomes]
rs35185431	0.88[ASN][1000 genomes]
rs35203092	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35402416	0.83[EUR][1000 genomes]
rs35776557	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35807655	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35940587	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36079497	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821053	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55753459	0.94[ASN][1000 genomes]
rs55817781	0.91[EUR][1000 genomes]
rs6543088	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap]
rs6543111	0.85[ASN][1000 genomes]
rs6707719	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6707750	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6712078	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6713504	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6718982	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721323	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs6721467	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6728312	0.88[ASN][1000 genomes]
rs6738401	0.94[ASN][1000 genomes]
rs6751727	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6755021	0.94[ASN][1000 genomes]
rs6756969	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760008	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs68115667	1.00[ASN][1000 genomes]
rs6875	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap]
rs71429373	0.94[ASN][1000 genomes]
rs718159	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7557495	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570009	0.88[ASN][1000 genomes]
rs7578638	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582298	0.94[ASN][1000 genomes]
rs7591374	0.81[EUR][1000 genomes]
rs7593290	0.88[ASN][1000 genomes]
rs7594928	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7595039	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7599043	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7605288	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784011	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9808558	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9973490	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7588227	ADRA2B	cis	parietal	SCAN
rs7588227	TEKT4	cis	cerebellum	SCAN
rs7588227	INPP4A	cis	cerebellum	SCAN
rs7588227	LONRF2	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98553200-98565800	Weak transcription	Small Intestine	intestine
2	chr2:98553800-98562400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr2:98553800-98565800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:98554000-98565800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:98554000-98570200	Weak transcription	Primary B cells from cord blood	blood
6	chr2:98554200-98563000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:98554400-98565400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr2:98559800-98567800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:98560200-98566400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:98561200-98562400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:98561400-98562200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:98561400-98566800	Weak transcription	HSMMtube	muscle
13	chr2:98561600-98562200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:98561600-98562400	Enhancers	Stomach Mucosa	stomach
15	chr2:98561600-98562600	Enhancers	Fetal Lung	lung
16	chr2:98561600-98562600	Enhancers	NHDF-Ad	bronchial
17	chr2:98561800-98562400	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr2:98561800-98562400	Weak transcription	Right Ventricle	heart
19	chr2:98561800-98562600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:98561800-98562600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr2:98561800-98562600	Enhancers	Fetal Heart	heart
22	chr2:98561800-98563000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:98561800-98564200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:98561800-98564400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:98561800-98565800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:98561800-98566800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:98561800-98570200	Weak transcription	Primary T cells from cord blood	blood
28	chr2:98562000-98562200	Enhancers	HSMM	muscle
29	chr2:98562000-98562600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:98562000-98562600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:98562000-98562600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:98562000-98562600	Enhancers	Fetal Intestine Large	intestine
33	chr2:98562000-98562600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:98562000-98567400	Weak transcription	Brain Substantia Nigra	brain

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