Variant report

Variant	rs11652530
Chromosome Location	chr17:67126564-67126565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:67124204..67127688-chr17:67128556..67131648,3	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10775358	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10775359	0.82[ASN][1000 genomes]
rs1158495	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11656539	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11659091	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs12162136	0.84[EUR][1000 genomes]
rs12453914	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12601388	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12939282	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952117	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12953127	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs1558166	0.86[ASN][1000 genomes]
rs16973567	0.86[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1968100	0.84[ASN][1000 genomes]
rs1974576	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1974577	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1990335	0.84[EUR][1000 genomes]
rs2041170	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041171	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108738	0.82[ASN][1000 genomes]
rs2190900	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2215148	0.85[ASN][1000 genomes]
rs2364986	0.86[ASN][1000 genomes]
rs2364993	0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs3744489	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4141177	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4334355	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577157	0.83[ASN][1000 genomes]
rs4603621	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968785	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4968838	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968839	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968843	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4968849	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs4968851	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs5025273	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6501183	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207609	0.84[EUR][1000 genomes]
rs7208586	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7210259	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7213831	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7214079	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7216899	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7217887	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs740518	0.86[ASN][1000 genomes]
rs740520	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7503217	0.84[EUR][1000 genomes]
rs763920	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs8064595	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066449	0.86[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs8074654	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs8077252	0.80[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8077551	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs8078314	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8079981	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8080863	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9303012	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs976698	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs981452	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9892172	0.84[ASN][1000 genomes]
rs9898868	0.84[ASN][1000 genomes]
rs9899837	0.84[ASN][1000 genomes]
rs9902643	0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9904672	0.84[ASN][1000 genomes]
rs9911770	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9912127	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs9916084	0.82[ASN][1000 genomes]
rs9916693	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs997781	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv575930	chr17:67120025-67212031	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11652530	CACNG5	cis	cerebellum	SCAN
rs11652530	ABCA6	cis	cerebellum	SCAN
rs11652530	ABCA6	cis	parietal	SCAN
rs11652530	MRC2	cis	parietal	SCAN
rs11652530	ABCA9	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67077800-67137800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr17:67087000-67130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr17:67091200-67131400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr17:67091600-67130000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr17:67092200-67137600	Weak transcription	Brain Anterior Caudate	brain
6	chr17:67095800-67131000	Weak transcription	Fetal Muscle Leg	muscle
7	chr17:67096200-67143400	Weak transcription	Psoas Muscle	Psoas
8	chr17:67096400-67134000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr17:67097000-67133800	Weak transcription	Colon Smooth Muscle	Colon
10	chr17:67099000-67131600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:67101200-67143400	Weak transcription	Pancreas	Pancrea
12	chr17:67106400-67131400	Weak transcription	Left Ventricle	heart
13	chr17:67109600-67129200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:67114600-67162800	Weak transcription	Brain Angular Gyrus	brain
15	chr17:67115600-67134000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr17:67115800-67130600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr17:67117800-67130400	Weak transcription	Ovary	ovary
18	chr17:67119000-67131000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr17:67119600-67131600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr17:67120000-67138000	Weak transcription	Small Intestine	intestine
21	chr17:67121800-67137800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr17:67123200-67129000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr17:67123800-67136400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:67124200-67130200	Weak transcription	NHDF-Ad	bronchial
25	chr17:67124600-67137600	Weak transcription	Fetal Stomach	stomach
26	chr17:67124800-67150000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr17:67125200-67126600	Weak transcription	Fetal Lung	lung
28	chr17:67125800-67128200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr17:67126200-67128400	Enhancers	Liver	Liver
30	chr17:67126400-67126800	Strong transcription	Adipose Nuclei	Adipose

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