Variant report

Variant	rs7089668
Chromosome Location	chr10:97608422-97608423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10509686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509695	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10786239	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786247	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs10882649	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs10882661	0.91[ASN][1000 genomes]
rs10882671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188417	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs11188444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11188455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188464	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188480	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188484	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11188489	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188501	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11188504	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]
rs11188506	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188509	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188516	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188531	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11593044	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11593761	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597321	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11598475	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12354848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12358481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12359343	0.86[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap]
rs12359366	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12360382	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12411569	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1340837	0.85[CEU][hapmap]
rs17382898	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17461546	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs17462179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17553401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1891535	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1891536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935814	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935815	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861154	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3181122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3192654	0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258314	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs4320886	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4344425	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4402217	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463786	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512761	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568937	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4918966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4918970	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918972	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55801606	0.83[ASN][1000 genomes]
rs61869573	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61869591	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074866	0.90[EUR][1000 genomes]
rs7091088	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895056	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7896876	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918339	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking 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 target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv895907	chr10:97529318-97686064	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv895908	chr10:97544513-97724247	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS 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 target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7089668	FRAT2	cis	cerebellum	SCAN
rs7089668	ANKRD2	cis	cerebellum	SCAN
rs7089668	ENTPD1	cis	lymphoblastoid	seeQTL
rs7089668	ALDH18A1	cis	cerebellum	SCAN
rs7089668	ENTPD1	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97592600-97632800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:97597200-97627200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr10:97597400-97624600	Weak transcription	Placenta	Placenta
4	chr10:97597400-97627400	Weak transcription	Brain Angular Gyrus	brain
5	chr10:97597600-97609600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr10:97597600-97620600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:97600600-97628600	Weak transcription	Colonic Mucosa	Colon
8	chr10:97601200-97624600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:97601600-97624400	Weak transcription	Fetal Intestine Large	intestine
10	chr10:97601600-97635600	Weak transcription	Fetal Brain Male	brain
11	chr10:97601800-97608800	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:97601800-97609200	Strong transcription	GM12878-XiMat	blood
13	chr10:97601800-97624600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr10:97601800-97626000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr10:97601800-97626400	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:97601800-97627200	Weak transcription	Liver	Liver
17	chr10:97601800-97635400	Weak transcription	Brain Substantia Nigra	brain
18	chr10:97601800-97647800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr10:97602200-97611000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr10:97602400-97610800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr10:97602400-97611000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr10:97602400-97655400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr10:97602600-97610800	Strong transcription	Primary B cells from cord blood	blood
24	chr10:97603000-97624800	Weak transcription	Fetal Intestine Small	intestine
25	chr10:97603200-97624800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr10:97603800-97620200	Weak transcription	Spleen	Spleen
27	chr10:97604400-97609800	Strong transcription	Aorta	Aorta
28	chr10:97605400-97620800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr10:97606800-97610600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr10:97606800-97611000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr10:97607000-97610200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr10:97607200-97610200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr10:97607200-97610600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr10:97607200-97610600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr10:97607400-97609600	Strong transcription	Brain Anterior Caudate	brain
36	chr10:97607600-97608600	Strong transcription	Fetal Stomach	stomach
37	chr10:97608200-97610400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr10:97608400-97620000	Weak transcription	Left Ventricle	heart
39	chr10:97608400-97620000	Weak transcription	Lung	lung
40	chr10:97608400-97620000	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links