Variant report

Variant	rs4147961
Chromosome Location	chr17:66937261-66937262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11077818	0.87[EUR][1000 genomes]
rs11077819	0.88[EUR][1000 genomes]
rs11650211	0.85[EUR][1000 genomes]
rs11655684	0.85[EUR][1000 genomes]
rs11656365	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11658489	0.85[EUR][1000 genomes]
rs1860445	0.88[EUR][1000 genomes]
rs1860446	0.85[EUR][1000 genomes]
rs1990334	0.86[EUR][1000 genomes]
rs2191214	0.88[EUR][1000 genomes]
rs3744498	0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs3744499	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs4147948	0.85[GIH][hapmap];0.81[TSI][hapmap]
rs4147951	0.85[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs4147953	0.85[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs4147954	0.88[EUR][1000 genomes]
rs4147955	0.85[EUR][1000 genomes]
rs4147957	0.85[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs4147959	0.87[EUR][1000 genomes]
rs4147960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147963	0.89[EUR][1000 genomes]
rs4147964	0.88[EUR][1000 genomes]
rs4147968	0.81[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs4147970	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs4147971	0.87[EUR][1000 genomes]
rs4147972	0.87[EUR][1000 genomes]
rs4147973	0.80[EUR][1000 genomes]
rs4147974	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968827	0.88[EUR][1000 genomes]
rs4968977	0.88[EUR][1000 genomes]
rs4968978	0.87[EUR][1000 genomes]
rs7225473	0.88[EUR][1000 genomes]
rs8068037	0.87[EUR][1000 genomes]
rs8070184	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8072891	0.87[EUR][1000 genomes]
rs8079972	0.87[EUR][1000 genomes]
rs8082257	0.86[EUR][1000 genomes]
rs887380	1.00[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];0.98[EUR][1000 genomes];1.00[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	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	nsv1061151	chr17:66881617-66973917	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv908700	chr17:66885526-66985992	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv908701	chr17:66888346-66978319	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1066412	chr17:66897540-66954067	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv1846502	chr17:66899261-66966274	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv1849165	chr17:66899261-66978319	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv908703	chr17:66904001-66978319	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv908704	chr17:66925324-66959710	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4147961	ABCA6	cis	parietal	SCAN
rs4147961	EFCAB3	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66907000-66940800	Weak transcription	Spleen	Spleen
2	chr17:66908000-66949000	Weak transcription	Right Ventricle	heart
3	chr17:66916200-66949000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:66916200-66949400	Weak transcription	Fetal Muscle Leg	muscle
5	chr17:66916400-66938600	Weak transcription	Psoas Muscle	Psoas
6	chr17:66916400-66949200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr17:66916400-66949400	Weak transcription	Osteobl	bone
8	chr17:66921200-66941000	Weak transcription	Fetal Heart	heart
9	chr17:66923000-66939000	Weak transcription	K562	blood
10	chr17:66923400-66938600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:66927200-66937400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr17:66927400-66938400	Weak transcription	Left Ventricle	heart
13	chr17:66927400-66948800	Weak transcription	Brain Substantia Nigra	brain
14	chr17:66931600-66948800	Weak transcription	Ovary	ovary
15	chr17:66933000-66938200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:66933400-66948800	Weak transcription	Fetal Lung	lung
17	chr17:66933800-66949400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:66936200-66948800	Weak transcription	Adipose Nuclei	Adipose
19	chr17:66936400-66939600	Weak transcription	HepG2	liver
20	chr17:66936800-66948800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr17:66937200-66940200	Enhancers	Liver	Liver

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