Variant report

Variant	rs336402
Chromosome Location	chr4:143068790-143068791
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1219266	0.81[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs1219268	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs1219269	0.81[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs1219270	0.92[ASW][hapmap];0.81[CEU][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs1219275	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs1390994	0.84[ASW][hapmap];0.81[CEU][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs1497139	0.87[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1532450	0.80[CEU][hapmap]
rs182862	0.80[AMR][1000 genomes]
rs1907113	0.81[CEU][hapmap]
rs1907119	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs1907135	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1948323	0.81[CEU][hapmap]
rs2130685	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs2172023	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs2627813	0.85[YRI][hapmap]
rs2627817	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs2636632	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs2636637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636643	0.81[CEU][hapmap]
rs2636656	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs2636660	0.81[CEU][hapmap]
rs3102438	0.81[CEU][hapmap]
rs3102439	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs3113511	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs336384	0.81[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]
rs336391	0.92[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs336393	0.94[CEU][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs336394	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs336396	0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs336404	0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336408	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992257	0.84[ASW][hapmap];0.86[MKK][hapmap];0.87[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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830097	chr4:142949705-143136372	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv830098	chr4:143050143-143234384	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143018800-143109600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:143043400-143089000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:143049800-143114400	Weak transcription	Right Ventricle	heart
4	chr4:143050000-143079600	Weak transcription	NHDF-Ad	bronchial
5	chr4:143051400-143093400	Weak transcription	Left Ventricle	heart
6	chr4:143051800-143070600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:143052400-143081400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:143052400-143111600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:143052600-143081400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:143052600-143094600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:143057600-143078800	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:143057800-143070200	Weak transcription	Fetal Heart	heart
13	chr4:143057800-143079000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:143057800-143114400	Weak transcription	Aorta	Aorta
15	chr4:143058000-143181000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:143060400-143072400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:143061000-143081000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:143061200-143069400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:143061200-143079000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:143061200-143079200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:143061800-143069200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:143061800-143102200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:143062200-143068800	Weak transcription	HSMMtube	muscle
24	chr4:143062200-143081200	Weak transcription	NHEK	skin
25	chr4:143063600-143069800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:143064200-143078800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:143064200-143080200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:143064200-143093200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:143064400-143069800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:143064400-143078600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:143064600-143068800	Weak transcription	HSMM	muscle
32	chr4:143064600-143069200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:143065600-143070400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr4:143066000-143073400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr4:143066200-143070200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:143066200-143072600	Strong transcription	Primary T cells from cord blood	blood
37	chr4:143066200-143074400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:143066600-143071000	Weak transcription	HMEC	breast
39	chr4:143067000-143071200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:143067200-143069200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:143067200-143070800	Weak transcription	Dnd41	blood
42	chr4:143067400-143068800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:143068200-143069200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr4:143068600-143069200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:143068600-143070200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links