Variant report

Variant	rs10947535
Chromosome Location	chr6:34975969-34975970
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10807143	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947533	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10947534	0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11755713	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16895035	0.87[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs16895354	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1737724	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2030611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2395601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395602	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3734258	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3734259	0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs3756859	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs3777750	0.88[JPT][hapmap]
rs3800443	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3800448	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3800450	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3800452	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3800453	0.87[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3822923	0.93[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs56140217	0.82[ASN][1000 genomes]
rs56248791	0.93[ASN][1000 genomes]
rs6457799	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6913108	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6918498	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs6941065	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs7740148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7751820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752468	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs847844	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs847845	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs847861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs847862	0.93[ASW][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9380465	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9380466	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9380467	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9380468	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9380470	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9380476	0.93[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs9380480	0.82[ASN][1000 genomes]
rs9380481	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9784889	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv885797	chr6:34791027-34980601	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10947535	PRDM7	trans	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34925600-34984800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:34926800-34992200	Weak transcription	Small Intestine	intestine
3	chr6:34932400-34981800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:34939400-34978200	Weak transcription	Psoas Muscle	Psoas
5	chr6:34939400-35016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:34959200-34979000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:34960200-34979200	Weak transcription	HUVEC	blood vessel
8	chr6:34960200-34988200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:34961000-34985200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:34961200-34983400	Weak transcription	Fetal Kidney	kidney
11	chr6:34961600-34982200	Weak transcription	Right Ventricle	heart
12	chr6:34962200-34982200	Weak transcription	Hela-S3	cervix
13	chr6:34962200-34984800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:34962800-34978800	Weak transcription	Fetal Lung	lung
15	chr6:34962800-34983600	Weak transcription	Osteobl	bone
16	chr6:34962800-34985200	Weak transcription	Brain Germinal Matrix	brain
17	chr6:34963000-34976000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:34963000-34976000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:34963000-34978000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:34963000-34979400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:34963000-34982200	Weak transcription	Aorta	Aorta
22	chr6:34963000-34982200	Weak transcription	Pancreas	Pancrea
23	chr6:34963000-34982400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:34963000-34982400	Weak transcription	Fetal Stomach	stomach
25	chr6:34963000-34982600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:34963000-34985000	Weak transcription	Fetal Brain Female	brain
27	chr6:34963000-34985200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:34963000-34985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr6:34963000-34985600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:34963000-34985600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:34963000-34985600	Weak transcription	NHEK	skin
32	chr6:34963000-34987800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:34963000-34989400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:34963200-34982200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:34963600-34978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:34963600-34978800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:34963600-34978800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:34963600-34981600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:34963600-34982000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:34963600-34982000	Weak transcription	Adipose Nuclei	Adipose
41	chr6:34963600-34983400	Weak transcription	Colonic Mucosa	Colon
42	chr6:34963600-34990000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:34963600-35006600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:34964200-34985400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:34965600-34976000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:34965800-34985400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:34965800-34985400	Weak transcription	HepG2	liver
48	chr6:34966000-34978600	Weak transcription	HSMM	muscle
49	chr6:34966000-34982200	Weak transcription	Left Ventricle	heart
50	chr6:34966000-34985400	Weak transcription	Primary hematopoietic stem cells	blood

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