Variant report

Variant	rs9845950
Chromosome Location	chr3:136356598-136356599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136346602..136349491-chr3:136356349..136359301,2	K562	blood:
2	chr3:136344155..136348284-chr3:136354109..136358125,4	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10513014	0.95[CEU][hapmap]
rs12635723	0.85[LWK][hapmap];0.92[YRI][hapmap]
rs13433980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1484250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843991	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs1872240	0.81[EUR][1000 genomes]
rs28682370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34992220	0.86[CEU][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs35375192	0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap]
rs35644083	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs3932048	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs4336059	0.83[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4402873	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4678438	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs55993001	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56047785	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59931907	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6439642	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs6439655	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs66810260	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6763239	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6765239	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6771713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6772759	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6782151	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788346	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6789329	0.91[CEU][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap]
rs6789541	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6799699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6800969	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6804194	0.83[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap]
rs6806795	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs699165	0.81[LWK][hapmap];0.82[YRI][hapmap]
rs7612160	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7621017	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7621970	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7623824	0.94[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7626418	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7627292	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7629905	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7644346	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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]
rs7644471	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9812319	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs9818372	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9820513	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9828068	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9832572	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834631	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9839574	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs9845762	0.85[LWK][hapmap];0.92[YRI][hapmap]
rs9854084	0.82[YRI][hapmap]
rs9868120	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs9869361	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869957	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9876771	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9877786	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9881078	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9845950	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136308000-136357400	Weak transcription	Lung	lung
2	chr3:136315800-136361000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:136316000-136364400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:136320800-136356800	Weak transcription	Ovary	ovary
5	chr3:136323400-136362000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:136324200-136363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:136327400-136357400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:136335600-136357400	Weak transcription	Psoas Muscle	Psoas
9	chr3:136336200-136364800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:136345800-136364000	Weak transcription	Small Intestine	intestine
11	chr3:136347000-136361200	Weak transcription	Left Ventricle	heart
12	chr3:136347200-136368400	Weak transcription	Fetal Intestine Small	intestine
13	chr3:136347400-136358400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:136347400-136364000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:136347600-136367200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:136348200-136365000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:136348600-136364600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:136348800-136363800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:136348800-136373600	Weak transcription	Thymus	Thymus
20	chr3:136349800-136357400	Weak transcription	Fetal Thymus	thymus
21	chr3:136349800-136372400	Weak transcription	Dnd41	blood
22	chr3:136350600-136372200	Weak transcription	Primary T cells from cord blood	blood
23	chr3:136351600-136364600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:136351600-136364800	Weak transcription	Pancreas	Pancrea
25	chr3:136351600-136376200	Weak transcription	Esophagus	oesophagus
26	chr3:136351800-136364000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:136351800-136364600	Weak transcription	Right Ventricle	heart
28	chr3:136352000-136364000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:136352400-136357800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:136352400-136361600	Weak transcription	Right Atrium	heart
31	chr3:136352400-136371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:136352400-136371600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:136352400-136371800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:136354400-136364000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:136355600-136356800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr3:136356000-136364600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:136356200-136356600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:136356400-136356800	Enhancers	Brain Anterior Caudate	brain
39	chr3:136356400-136357800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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