Variant report

Variant	rs9860801
Chromosome Location	chr3:136088038-136088039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136085761..136088566-chr3:136470764..136472314,2	K562	blood:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1279425	0.82[YRI][hapmap]
rs16843991	0.95[CEU][hapmap];0.89[YRI][hapmap]
rs2305265	1.00[CHD][hapmap]
rs28396702	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28812220	0.90[EUR][1000 genomes]
rs34165586	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34523567	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35058853	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35375192	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35644083	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]
rs3932048	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap]
rs4678428	0.82[YRI][hapmap]
rs5026242	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs548288	0.82[YRI][hapmap]
rs55797013	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56251259	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs576771	0.82[YRI][hapmap]
rs6439638	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6439642	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs67214626	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6766450	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6776841	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6783337	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6785225	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6804194	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7612160	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs7620314	0.81[CEU][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap]
rs7622833	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7644471	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs9809184	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9811261	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9811490	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9812319	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9819496	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9826146	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes]
rs9831321	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9833162	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9843348	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9843801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9850383	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9853387	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]
rs9854328	0.80[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[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9872326	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9860801	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
2	chr3:136047600-136098000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:136055600-136100800	Weak transcription	Spleen	Spleen
5	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:136063600-136097000	Weak transcription	Colonic Mucosa	Colon
8	chr3:136063600-136105600	Weak transcription	Gastric	stomach
9	chr3:136063600-136110600	Weak transcription	Small Intestine	intestine
10	chr3:136063600-136139200	Weak transcription	Pancreas	Pancrea
11	chr3:136063800-136095200	Weak transcription	Lung	lung
12	chr3:136065400-136097200	Weak transcription	HepG2	liver
13	chr3:136067600-136109000	Weak transcription	HUVEC	blood vessel
14	chr3:136068600-136103800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:136069400-136121200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:136069600-136107400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:136069600-136138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:136069600-136139400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:136069800-136088800	Weak transcription	HMEC	breast
20	chr3:136069800-136106600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:136069800-136118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:136070400-136095000	Weak transcription	NH-A	brain
24	chr3:136070600-136101000	Weak transcription	Right Ventricle	heart
25	chr3:136070600-136105800	Weak transcription	Psoas Muscle	Psoas
26	chr3:136070800-136095200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:136070800-136096800	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:136070800-136096800	Weak transcription	HSMMtube	muscle
29	chr3:136070800-136099600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:136070800-136112200	Weak transcription	Aorta	Aorta
31	chr3:136070800-136121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:136072600-136098800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:136072800-136097000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:136072800-136100400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:136073000-136093800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:136075000-136137800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:136075400-136093600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:136075400-136093800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:136075400-136108000	Weak transcription	Fetal Brain Female	brain
40	chr3:136075600-136094200	Weak transcription	Left Ventricle	heart
41	chr3:136075600-136097000	Weak transcription	Fetal Lung	lung
42	chr3:136075600-136105800	Weak transcription	Ovary	ovary
43	chr3:136075800-136094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:136075800-136099000	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
46	chr3:136076600-136088800	Strong transcription	Dnd41	blood
47	chr3:136078200-136096000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:136081200-136093600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:136081200-136118800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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