Variant report

Variant	rs10988804
Chromosome Location	chr9:98720919-98720920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10983321	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10988581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10988792	0.90[ASW][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11787559	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11790370	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11790491	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793298	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11794054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001	0.89[GIH][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap]
rs12683310	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs12683634	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12685221	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12685318	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12685807	0.89[GIH][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap]
rs12686222	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12686457	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1360064	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16910262	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16910296	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16910298	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16910418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1831228	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1999023	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2026032	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2069053	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2274653	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2274654	0.90[ASW][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34533243	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3780574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802438	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4532708	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742775	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742781	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743372	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743391	0.90[AFR][1000 genomes]
rs4743400	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4743417	0.82[EUR][1000 genomes]
rs4743418	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743419	0.93[AFR][1000 genomes]
rs4743436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743472	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs591486	0.81[YRI][hapmap]
rs7048414	0.90[CEU][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73536517	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73656544	0.84[EUR][1000 genomes]
rs7868270	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1035723	chr9:98701628-98734356	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10988804	LINC00476	cis	Esophagus Mucosa	GTEx
rs10988804	LINC00476	cis	Whole Blood	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
2	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:98687800-98726000	Weak transcription	Gastric	stomach
4	chr9:98695800-98742400	Weak transcription	NHLF	lung
5	chr9:98705400-98734200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
7	chr9:98706800-98734000	Weak transcription	Hela-S3	cervix
8	chr9:98709800-98727800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:98710000-98734200	Weak transcription	HMEC	breast
10	chr9:98710000-98735000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:98710400-98741400	Weak transcription	Brain Anterior Caudate	brain
12	chr9:98711000-98722000	Weak transcription	Brain Germinal Matrix	brain
13	chr9:98711000-98743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
15	chr9:98716600-98734400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr9:98718000-98722600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:98718600-98729600	Weak transcription	NHDF-Ad	bronchial
18	chr9:98718800-98729400	Weak transcription	HepG2	liver
19	chr9:98719000-98733800	Weak transcription	NHEK	skin
20	chr9:98719000-98738600	Weak transcription	Aorta	Aorta
21	chr9:98719000-98743800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr9:98719000-98751400	Weak transcription	Stomach Mucosa	stomach
23	chr9:98719200-98722800	Weak transcription	Fetal Brain Male	brain
24	chr9:98719200-98723000	Weak transcription	HSMMtube	muscle
25	chr9:98719200-98725000	Weak transcription	Fetal Stomach	stomach
26	chr9:98719200-98726000	Weak transcription	Primary B cells from cord blood	blood
27	chr9:98719200-98726000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:98719200-98728800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr9:98719200-98729200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr9:98719200-98733600	Weak transcription	Fetal Intestine Large	intestine
31	chr9:98719200-98734200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:98719200-98734200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:98719200-98734200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr9:98719200-98734200	Weak transcription	Esophagus	oesophagus
35	chr9:98719200-98734200	Weak transcription	Lung	lung
36	chr9:98719200-98734200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr9:98719200-98734200	Weak transcription	Thymus	Thymus
38	chr9:98719200-98734200	Weak transcription	K562	blood
39	chr9:98719200-98734800	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:98719200-98744000	Weak transcription	Brain Substantia Nigra	brain
41	chr9:98719200-98744400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:98719200-98749600	Weak transcription	Fetal Intestine Small	intestine
43	chr9:98719200-98749800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:98719200-98752800	Weak transcription	Pancreas	Pancrea
45	chr9:98719200-98764200	Weak transcription	Spleen	Spleen
46	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:98719400-98722000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:98719400-98722000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:98719400-98722000	Weak transcription	Fetal Muscle Leg	muscle
50	chr9:98719400-98722000	Weak transcription	HSMM	muscle

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