Variant report

Variant	rs9839574
Chromosome Location	chr3:136376035-136376036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10513014	0.95[CEU][hapmap]
rs12493906	1.00[JPT][hapmap]
rs12635723	0.89[YRI][hapmap]
rs13433980	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs1484250	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs16843991	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs34804893	0.81[GIH][hapmap]
rs34992220	0.86[CEU][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs35644083	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap]
rs3931416	0.87[LWK][hapmap]
rs3932048	0.91[CEU][hapmap];0.85[YRI][hapmap]
rs4336059	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs4678438	0.89[YRI][hapmap]
rs6439642	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs6765239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs6771713	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs6782151	0.83[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap]
rs6789329	0.91[CEU][hapmap];0.85[GIH][hapmap]
rs6799699	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs6800969	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7612160	0.95[CEU][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap]
rs7623824	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs7644346	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs7644471	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs9812319	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap]
rs9820513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs9845762	0.89[YRI][hapmap]
rs9845950	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs9869957	1.00[CEU][hapmap];1.00[YRI][hapmap]

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	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1008866	chr3:136364511-136427790	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9839574	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136351600-136376200	Weak transcription	Esophagus	oesophagus
2	chr3:136357800-136387400	Weak transcription	Fetal Thymus	thymus
3	chr3:136364800-136377800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:136365000-136396400	Weak transcription	Gastric	stomach
5	chr3:136365200-136381400	Weak transcription	Pancreas	Pancrea
6	chr3:136368200-136385000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:136369000-136386800	Weak transcription	Lung	lung
8	chr3:136370600-136385400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:136370800-136382800	Weak transcription	Ovary	ovary
10	chr3:136372000-136383200	Weak transcription	Aorta	Aorta
11	chr3:136373800-136376200	Weak transcription	NHEK	skin
12	chr3:136373800-136377600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:136373800-136382600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:136374200-136376200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:136374200-136377800	Weak transcription	Fetal Kidney	kidney
16	chr3:136374400-136376400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:136374400-136382600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:136374400-136387400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:136374400-136390000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:136374600-136378200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:136374600-136381200	Weak transcription	Fetal Stomach	stomach
22	chr3:136374600-136384200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:136374600-136387400	Weak transcription	Primary T cells from cord blood	blood
24	chr3:136374600-136389400	Weak transcription	Fetal Intestine Small	intestine
25	chr3:136374800-136377800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:136374800-136383400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:136374800-136390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:136375600-136390400	Weak transcription	Dnd41	blood

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