Variant report

Variant	rs9853387
Chromosome Location	chr3:136038988-136038989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1279425	0.82[YRI][hapmap]
rs16843991	0.95[CEU][hapmap];0.89[YRI][hapmap]
rs2305265	1.00[CHD][hapmap]
rs28396702	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28812220	0.93[EUR][1000 genomes]
rs34165586	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34523567	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35058853	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35375192	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35644083	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs3732519	1.00[CHD][hapmap]
rs3755636	0.82[YRI][hapmap]
rs3821444	1.00[CHD][hapmap]
rs4678428	0.82[YRI][hapmap]
rs5026242	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs548288	0.82[YRI][hapmap]
rs55797013	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56251259	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs576771	0.82[YRI][hapmap]
rs6439638	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6439642	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs67214626	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6766450	0.83[EUR][1000 genomes]
rs6776841	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6783337	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6785225	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6804194	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7620314	0.81[CEU][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap]
rs7622833	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809184	0.81[EUR][1000 genomes]
rs9811261	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9811490	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9812319	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs9812513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9819496	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9826146	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[EUR][1000 genomes]
rs9831321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9833162	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9843348	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9850383	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9854328	0.81[EUR][1000 genomes]
rs9860801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9868120	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs9872326	0.95[EUR][1000 genomes]

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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4025	chr3:136017458-136065622	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9853387	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:135981200-136052000	Weak transcription	NH-A	brain
3	chr3:135998000-136040200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
5	chr3:136014200-136040000	Weak transcription	Small Intestine	intestine
6	chr3:136016800-136045600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:136017000-136040000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:136018200-136051400	Weak transcription	A549	lung
9	chr3:136020200-136039000	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:136020200-136040200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:136020200-136045200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:136020400-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:136020400-136045200	Weak transcription	Colonic Mucosa	Colon
14	chr3:136020600-136045000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:136020600-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:136020800-136040200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:136020800-136040200	Weak transcription	Esophagus	oesophagus
18	chr3:136020800-136042200	Weak transcription	Placenta	Placenta
19	chr3:136020800-136043000	Weak transcription	HSMM	muscle
20	chr3:136020800-136045000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:136021000-136040000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:136021000-136045400	Weak transcription	Gastric	stomach
23	chr3:136021000-136045600	Weak transcription	Osteobl	bone
24	chr3:136021200-136039800	Weak transcription	NHEK	skin
25	chr3:136021200-136040000	Weak transcription	Thymus	Thymus
26	chr3:136030600-136040200	Weak transcription	Pancreas	Pancrea
27	chr3:136032800-136055400	Weak transcription	HUVEC	blood vessel
28	chr3:136035400-136039000	Strong transcription	Left Ventricle	heart
29	chr3:136035600-136039000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:136035600-136040200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:136035600-136040600	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:136035800-136039000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:136036400-136044200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:136036800-136040000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:136036800-136043400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:136037000-136040400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:136037000-136041600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr3:136037000-136045200	Weak transcription	Brain Angular Gyrus	brain
39	chr3:136037200-136040000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:136037200-136040200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:136037200-136040200	Weak transcription	Lung	lung
42	chr3:136037200-136045200	Weak transcription	Fetal Stomach	stomach
43	chr3:136037600-136039400	ZNF genes & repeats	Fetal Brain Female	brain
44	chr3:136037600-136045200	Weak transcription	K562	blood
45	chr3:136037600-136045400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:136037800-136041000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:136037800-136042200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:136038000-136040000	Weak transcription	Ovary	ovary
49	chr3:136038000-136042600	ZNF genes & repeats	Dnd41	blood
50	chr3:136038200-136039000	ZNF genes & repeats	Aorta	Aorta

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