Variant report

Variant	rs4968839
Chromosome Location	chr17:67125840-67125841
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: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10775358	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs10775359	0.82[ASN][1000 genomes]
rs11077942	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs1158495	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11652530	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]
rs11656539	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs12162136	0.93[EUR][1000 genomes]
rs12453914	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12453921	0.81[CEU][hapmap]
rs12601388	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12939282	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12940298	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12952117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12953127	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs1558166	0.85[ASN][1000 genomes]
rs16973567	0.87[CEU][hapmap];0.85[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1968100	0.84[ASN][1000 genomes]
rs1974576	0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1974577	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs1990335	0.93[EUR][1000 genomes]
rs2041170	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041171	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108738	0.82[ASN][1000 genomes]
rs2190900	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2215148	0.84[ASN][1000 genomes]
rs2302132	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs2302133	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs2302134	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs2364986	0.85[ASN][1000 genomes]
rs2364993	0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs3744489	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4141177	0.85[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4334355	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4577157	0.82[ASN][1000 genomes]
rs4603621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968785	0.90[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs4968838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968843	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs4968849	0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs4968851	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs5025273	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs6501183	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7207609	0.92[EUR][1000 genomes]
rs7208586	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7210259	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs7213831	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7214079	0.85[CEU][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7216899	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7217887	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs740517	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs740518	0.85[ASN][1000 genomes]
rs740520	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs7503217	0.92[EUR][1000 genomes]
rs8064595	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8066449	0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[TSI][hapmap]
rs8074654	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs8077252	0.87[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs8077551	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs8078314	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8079981	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8080863	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs9303012	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs976698	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981452	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs9892172	0.84[ASN][1000 genomes]
rs9898868	0.84[ASN][1000 genomes]
rs9899837	0.84[ASN][1000 genomes]
rs9902643	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs9904672	0.84[ASN][1000 genomes]
rs9911770	0.85[CHB][hapmap]
rs9912127	0.86[CHD][hapmap];0.86[TSI][hapmap]
rs9916084	0.82[ASN][1000 genomes]
rs9916693	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997781	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4968839	ABCA6	cis	cerebellum	SCAN
rs4968839	CACNG5	cis	cerebellum	SCAN
rs4968839	ABCA9	cis	parietal	SCAN
rs4968839	ABCA6	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	chr17:67125200-67126200	Genic enhancers	Liver	Liver
28	chr17:67125200-67126400	Weak transcription	Adipose Nuclei	Adipose
29	chr17:67125200-67126600	Weak transcription	Fetal Lung	lung
30	chr17:67125800-67128200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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