Variant report

Variant	rs10975516
Chromosome Location	chr9:6247693-6247694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10118795	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10435816	0.86[JPT][hapmap]
rs1048274	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10758750	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10815383	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10815388	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10815390	0.88[ASN][1000 genomes]
rs10815394	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10815398	0.95[GIH][hapmap];0.92[MEX][hapmap]
rs10975497	0.85[JPT][hapmap]
rs10975499	0.81[ASN][1000 genomes]
rs10975509	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10975512	0.91[ASN][1000 genomes]
rs10975514	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10975515	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10975519	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10975520	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1113573	0.95[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11792139	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11792633	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336076	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12341955	0.88[ASN][1000 genomes]
rs12351913	0.83[ASN][1000 genomes]
rs12551256	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12683567	0.83[ASN][1000 genomes]
rs1317230	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330383	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1332290	0.81[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1375	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1412421	0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs16924171	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1929992	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4237163	0.88[ASN][1000 genomes]
rs4237164	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4742170	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7019575	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7025417	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7033258	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7034720	0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7044343	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7047921	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7849201	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7857724	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7871381	0.80[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs928414	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv613205	chr9:6032924-6332901	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv916394	chr9:6055497-6322471	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv892157	chr9:6093790-6322415	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers 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	28 gene(s)	inside rSNPs	diseases
8	nsv831496	chr9:6101763-6285088	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv521598	chr9:6142157-6291125	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv892158	chr9:6149006-6266440	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1027270	chr9:6152434-6328227	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv539968	chr9:6152434-6328227	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
14	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
16	nsv1019912	chr9:6224906-6257395	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10975516	RANBP6	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6229400-6251000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:6237200-6258400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:6238600-6252400	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:6239400-6255200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:6239400-6257600	Weak transcription	Brain Anterior Caudate	brain
6	chr9:6239600-6247800	Weak transcription	Fetal Intestine Large	intestine
7	chr9:6239800-6251600	Weak transcription	Gastric	stomach
8	chr9:6243200-6250600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:6243200-6255800	Weak transcription	Left Ventricle	heart
10	chr9:6243400-6256200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:6244800-6251000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:6246800-6248000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:6246800-6248000	Enhancers	HMEC	breast
14	chr9:6246800-6248000	Enhancers	NHEK	skin
15	chr9:6246800-6249000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:6247200-6248000	Enhancers	HepG2	liver
17	chr9:6247200-6249000	Enhancers	Fetal Intestine Small	intestine
18	chr9:6247200-6249000	Enhancers	HUVEC	blood vessel
19	chr9:6247600-6247800	Enhancers	Stomach Mucosa	stomach
20	chr9:6247600-6248600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:6247600-6248800	Enhancers	Duodenum Mucosa	Duodenum
22	chr9:6247600-6248800	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr9:6247600-6268800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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