Variant report

Variant	rs12539895
Chromosome Location	chr7:107091849-107091850
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10464499	0.92[ASN][1000 genomes]
rs10464620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10487271	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10953536	0.83[EUR][1000 genomes]
rs10953537	0.84[EUR][1000 genomes]
rs10953541	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11532774	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11766060	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11766131	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11770061	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12056231	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12532447	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12532514	0.83[EUR][1000 genomes]
rs12532849	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12533694	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12534124	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12535038	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12535093	0.83[EUR][1000 genomes]
rs12535258	0.94[CEU][hapmap]
rs12535761	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12535814	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12536603	0.83[EUR][1000 genomes]
rs12537011	0.84[EUR][1000 genomes]
rs12537785	0.84[EUR][1000 genomes]
rs13234124	0.86[ASN][1000 genomes]
rs17349904	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap]
rs17403088	0.86[CEU][hapmap];0.93[CHB][hapmap];0.94[ASN][1000 genomes]
rs17404067	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17428126	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17429825	0.84[EUR][1000 genomes]
rs17481621	0.94[ASN][1000 genomes]
rs17481842	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17482494	0.92[ASN][1000 genomes]
rs17482543	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17486	0.94[ASN][1000 genomes]
rs1978085	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1989814	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2249043	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs2283041	0.92[ASN][1000 genomes]
rs2299428	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2395859	0.84[EUR][1000 genomes]
rs2395880	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2395881	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2894459	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs34084719	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34523267	0.86[ASN][1000 genomes]
rs3757713	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3779497	0.97[ASN][1000 genomes]
rs3801963	0.94[CEU][hapmap]
rs3823959	0.84[EUR][1000 genomes]
rs3823960	0.84[EUR][1000 genomes]
rs4515482	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4727683	0.92[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4730239	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4730241	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4730242	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4730248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4730250	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs5002976	0.84[EUR][1000 genomes]
rs56949084	0.89[ASN][1000 genomes]
rs59782202	0.84[EUR][1000 genomes]
rs6945784	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6947674	0.90[ASN][1000 genomes]
rs6955488	0.92[ASN][1000 genomes]
rs6957186	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6958969	0.89[ASN][1000 genomes]
rs6964395	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964966	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6976759	0.92[ASN][1000 genomes]
rs6979198	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6979368	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763386	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs7781947	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7784906	0.92[ASN][1000 genomes]
rs7785962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7797791	0.89[ASN][1000 genomes]
rs7801317	0.92[ASN][1000 genomes]
rs7804979	0.83[EUR][1000 genomes]
rs7807154	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7809508	0.83[EUR][1000 genomes]
rs7810216	0.83[EUR][1000 genomes]
rs8180747	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv1019963	chr7:107033342-107188641	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv539052	chr7:107033342-107188641	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12539895	PRKAR2B	cis	cerebellum	SCAN
rs12539895	COG5	cis	parietal	SCAN
rs12539895	GPR22	Cis_1M	lymphoblastoid	RTeQTL
rs12539895	NRCAM	cis	parietal	SCAN
rs12539895	ATXN7L1	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107028200-107103800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:107035800-107133000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:107037800-107102200	Weak transcription	Ovary	ovary
4	chr7:107038800-107100600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:107050600-107102400	Weak transcription	Dnd41	blood
6	chr7:107050800-107100200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr7:107052000-107098600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr7:107052600-107126400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:107065000-107100600	Weak transcription	Thymus	Thymus
10	chr7:107067600-107119800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:107068200-107098400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr7:107068400-107104000	Weak transcription	Pancreas	Pancrea
13	chr7:107072400-107100000	Weak transcription	Gastric	stomach
14	chr7:107073000-107103600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:107076200-107099600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:107078400-107092400	Weak transcription	Fetal Thymus	thymus
17	chr7:107078800-107092400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:107079600-107108600	Weak transcription	Right Ventricle	heart
19	chr7:107080400-107099800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:107081000-107102600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr7:107081200-107103600	Weak transcription	Adipose Nuclei	Adipose
22	chr7:107082000-107100600	Weak transcription	Esophagus	oesophagus
23	chr7:107082800-107097800	Weak transcription	Fetal Intestine Small	intestine
24	chr7:107082800-107101000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:107082800-107104200	Weak transcription	Left Ventricle	heart
26	chr7:107082800-107109000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr7:107083400-107104200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:107083400-107104600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:107083400-107115400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:107084400-107109200	Weak transcription	Fetal Intestine Large	intestine
31	chr7:107085400-107101600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:107085800-107098200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:107086800-107098600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:107087400-107093600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:107087600-107092800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:107087600-107098400	Weak transcription	HSMM	muscle
37	chr7:107087600-107100800	Weak transcription	Spleen	Spleen
38	chr7:107087600-107103600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:107087600-107104000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:107087800-107097400	Weak transcription	Primary B cells from cord blood	blood
41	chr7:107087800-107103400	Weak transcription	Aorta	Aorta
42	chr7:107087800-107103600	Weak transcription	K562	blood
43	chr7:107087800-107112000	Weak transcription	NHDF-Ad	bronchial
44	chr7:107088000-107103600	Weak transcription	HSMMtube	muscle
45	chr7:107088000-107103800	Weak transcription	HMEC	breast
46	chr7:107088000-107103800	Weak transcription	NHEK	skin
47	chr7:107088200-107092400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:107088200-107100800	Weak transcription	Liver	Liver
49	chr7:107088600-107094600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr7:107088600-107126000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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