Variant report

Variant	rs3980310
Chromosome Location	chr10:95982015-95982016
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10882405	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10882407	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882409	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11187815	0.93[ASW][hapmap];0.81[CEU][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap]
rs11187825	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11187832	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11594064	0.81[CEU][hapmap]
rs1547643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2860749	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2860750	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736901	0.92[CEU][hapmap]
rs4113810	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4388804	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4477375	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7069316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7085875	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098833	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7910752	1.00[CEU][hapmap]
rs7914268	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816278	0.88[CEU][hapmap]
rs9325467	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9419788	0.96[CEU][hapmap];0.87[GIH][hapmap]
rs9663515	0.84[AMR][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	nsv1036676	chr10:95851376-96103876	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription 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	14 gene(s)	inside rSNPs	diseases
3	esv275010	chr10:95978397-95982802	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3980310	CYP2C19	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95960000-95991800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr10:95966600-95987000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:95967400-95988000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr10:95970800-96005800	Weak transcription	Colonic Mucosa	Colon
5	chr10:95971000-95994000	Weak transcription	Gastric	stomach
6	chr10:95971200-95983800	Weak transcription	Pancreas	Pancrea
7	chr10:95971200-95987200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr10:95973200-95983800	Weak transcription	Fetal Lung	lung
9	chr10:95973400-96012200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr10:95974200-96034000	Weak transcription	Colon Smooth Muscle	Colon
11	chr10:95974400-95987800	Weak transcription	Fetal Brain Female	brain
12	chr10:95974600-95983800	Weak transcription	Ovary	ovary
13	chr10:95974800-95982200	Weak transcription	Lung	lung
14	chr10:95975000-95982200	Weak transcription	Left Ventricle	heart
15	chr10:95975000-95985400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:95975200-95983200	Weak transcription	A549	lung
17	chr10:95975200-95992600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr10:95975400-95987000	Weak transcription	Aorta	Aorta
19	chr10:95975800-95982200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr10:95976400-95982200	Weak transcription	Fetal Muscle Leg	muscle
21	chr10:95977200-95983800	Weak transcription	Fetal Stomach	stomach
22	chr10:95979800-95984000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr10:95979800-95984000	Weak transcription	Osteobl	bone
24	chr10:95980000-95983400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr10:95980000-95984000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:95980000-95984000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:95980000-95985600	Weak transcription	Fetal Heart	heart
28	chr10:95980400-95982400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr10:95980600-95983000	Strong transcription	Fetal Intestine Small	intestine
30	chr10:95980600-95993800	Weak transcription	HSMMtube	muscle
31	chr10:95980800-95983200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr10:95981000-95987400	Weak transcription	Fetal Intestine Large	intestine
33	chr10:95981800-95982600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr10:95982000-95982200	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links