Variant report

Variant	rs35644083
Chromosome Location	chr3:136222468-136222469
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	chr3:136216747..136218980-chr3:136221671..136224312,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10513002	1.00[CHB][hapmap]
rs10513016	1.00[CHB][hapmap]
rs12635723	0.85[YRI][hapmap]
rs13433980	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs1484250	0.95[CEU][hapmap];0.92[YRI][hapmap]
rs16843978	1.00[CHB][hapmap]
rs16843991	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17199978	1.00[CHB][hapmap]
rs17266364	1.00[CHB][hapmap]
rs17365351	1.00[CHB][hapmap]
rs17466223	1.00[CHB][hapmap]
rs28396702	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34165586	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34804893	0.81[GIH][hapmap]
rs34962604	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375192	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3931416	1.00[CHB][hapmap];0.85[LWK][hapmap];0.81[AFR][1000 genomes]
rs3932048	0.95[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4336059	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs4402873	0.81[EUR][1000 genomes]
rs4678438	0.85[YRI][hapmap]
rs55993001	0.80[AMR][1000 genomes]
rs56040643	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56047785	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56125228	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56251259	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59931907	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6439638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs6439642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66810260	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6765239	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs6766450	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6769934	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772759	0.81[AFR][1000 genomes]
rs6773495	1.00[CHB][hapmap]
rs6773604	1.00[CHB][hapmap]
rs6776841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs6782151	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6783337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap]
rs6789541	0.81[EUR][1000 genomes]
rs6789761	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6799368	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800969	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs6804194	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6806795	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7612160	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7615706	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7620314	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs7621017	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7621970	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7623824	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs7627292	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7629905	0.82[AFR][1000 genomes]
rs7644346	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs7644471	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646563	1.00[CHB][hapmap]
rs7646723	1.00[CHB][hapmap]
rs7648591	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7650075	1.00[CHB][hapmap]
rs923001	1.00[CHB][hapmap]
rs9809184	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9812319	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9812513	1.00[CEU][hapmap]
rs9819496	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9820513	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs9828068	0.82[AFR][1000 genomes]
rs9831321	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9832572	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9833162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs9834631	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9839574	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]
rs9845762	0.85[YRI][hapmap]
rs9845950	0.89[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs9850383	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9853387	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs9858457	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860801	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs9866535	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868120	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9869361	0.81[AFR][1000 genomes]
rs9869957	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35644083	A4GNT	cis	parietal	SCAN
rs35644083	ZBTB38	cis	cerebellum	SCAN
rs35644083	SCN9A	trans	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136222800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:136176600-136224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:136176600-136224400	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:136176600-136231800	Weak transcription	Psoas Muscle	Psoas
6	chr3:136176600-136240000	Weak transcription	HMEC	breast
7	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:136176800-136228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
10	chr3:136177200-136236400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:136192200-136225600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:136193800-136231400	Weak transcription	NHLF	lung
15	chr3:136193800-136239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:136195000-136223000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:136195200-136231000	Weak transcription	Osteobl	bone
18	chr3:136195400-136231400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:136195400-136232000	Weak transcription	Right Ventricle	heart
20	chr3:136195400-136241800	Weak transcription	NH-A	brain
21	chr3:136195400-136250400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:136195600-136224000	Weak transcription	Brain Angular Gyrus	brain
24	chr3:136203000-136224600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:136208400-136230400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:136210200-136225800	Weak transcription	NHDF-Ad	bronchial
27	chr3:136210800-136229600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:136211600-136232000	Weak transcription	Fetal Kidney	kidney
29	chr3:136212200-136229200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:136212400-136223200	Weak transcription	Fetal Heart	heart
32	chr3:136212400-136231000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:136212400-136232000	Weak transcription	Aorta	Aorta
34	chr3:136212400-136241600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:136212400-136249600	Weak transcription	Lung	lung
36	chr3:136212600-136248200	Weak transcription	Esophagus	oesophagus
37	chr3:136213000-136231000	Weak transcription	Ovary	ovary
38	chr3:136213000-136239000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:136213000-136251000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:136213000-136252200	Weak transcription	Left Ventricle	heart
41	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:136213200-136224600	Weak transcription	Pancreas	Pancrea
43	chr3:136213200-136246000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:136213200-136246600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:136213400-136231000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:136214000-136239600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:136214000-136246200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:136214400-136238400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:136214600-136223400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:136214600-136231000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links