Variant report

Variant	rs9450763
Chromosome Location	chr6:88333894-88333895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88313795..88316259-chr6:88331275..88334158,3	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1052623	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1075665	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11962148	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11965562	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs11970493	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11970696	0.90[CHB][hapmap]
rs12524205	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12529993	0.86[ASN][1000 genomes]
rs12530371	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13214442	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs16879893	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2223877	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap]
rs2246051	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2246057	0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap]
rs2268996	0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs2295088	0.95[CHB][hapmap];0.81[CHD][hapmap]
rs2300898	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2300899	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2300900	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2300904	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs2300908	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs34513746	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3778671	0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs3818057	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4132446	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4354121	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707378	0.87[EUR][1000 genomes]
rs4707385	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707386	0.84[ASN][1000 genomes]
rs58305152	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454634	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6914244	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6915077	0.90[CHB][hapmap]
rs6927171	0.89[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs6928057	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs728582	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs7649	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs7761943	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9294384	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9294385	0.84[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[ASN][1000 genomes]
rs9444499	0.90[CHB][hapmap]
rs9444501	0.90[CHB][hapmap]
rs9444509	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9444513	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9444514	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444516	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444521	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9444531	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444534	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444536	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450681	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs9450686	0.90[CHB][hapmap]
rs9450693	0.90[CHB][hapmap]
rs9450694	0.83[CHB][hapmap]
rs9450697	0.89[CHB][hapmap]
rs9450698	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs9450699	1.00[CHB][hapmap]
rs9450700	1.00[CHB][hapmap]
rs9450708	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9450709	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9450716	0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs9450717	0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs9450728	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9450729	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9450734	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450735	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450740	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[ASN][1000 genomes]
rs9450741	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450743	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450749	0.87[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450750	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450751	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450756	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450760	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450773	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9474	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9450763	SLC35A1	cis	multi-tissue	Pritchard
rs9450763	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301000-88347200	Weak transcription	Small Intestine	intestine
3	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:88301400-88338400	Weak transcription	NHLF	lung
5	chr6:88301400-88354400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:88301400-88354600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:88302000-88347400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:88302000-88354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:88302000-88354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:88308800-88369800	Weak transcription	Fetal Brain Male	brain
12	chr6:88311400-88334600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:88312200-88371200	Weak transcription	NHEK	skin
14	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:88313800-88338200	Weak transcription	NHDF-Ad	bronchial
16	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
17	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
19	chr6:88315400-88334600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
22	chr6:88316800-88337800	Weak transcription	GM12878-XiMat	blood
23	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:88321200-88348400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:88321600-88350000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:88322000-88346200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:88322000-88352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:88322200-88334400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:88322600-88344800	Weak transcription	HMEC	breast
30	chr6:88322800-88338400	Weak transcription	Osteobl	bone
31	chr6:88322800-88344000	Weak transcription	Liver	Liver
32	chr6:88322800-88344800	Weak transcription	NH-A	brain
33	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:88323000-88342000	Weak transcription	K562	blood
35	chr6:88323000-88344600	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:88323000-88344800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:88323000-88346200	Weak transcription	Fetal Kidney	kidney
38	chr6:88323000-88366400	Weak transcription	A549	lung
39	chr6:88324000-88344000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:88324000-88347400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:88324000-88369800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:88324000-88385000	Weak transcription	Gastric	stomach
43	chr6:88324200-88337400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr6:88324200-88339200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:88324200-88339800	Weak transcription	Ovary	ovary
46	chr6:88324200-88344800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr6:88324200-88346000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:88324200-88346200	Weak transcription	Fetal Brain Female	brain
49	chr6:88324200-88350600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:88324200-88366600	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links