Variant report

Variant	rs336308
Chromosome Location	chr4:143020617-143020618
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	chr4:143020271..143023015-chr4:143028673..143031244,3	MCF-7	breast:
2	chr4:143018754..143020846-chr4:143024197..143025698,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1511247	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168059	0.87[CHB][hapmap];1.00[YRI][hapmap]
rs168061	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2201696	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2292393	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2667096	0.87[CHB][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap]
rs2667101	0.87[CHB][hapmap]
rs28714697	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs336292	0.86[CHB][hapmap]
rs336295	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336296	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs336297	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336298	0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap]
rs336300	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs336307	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs336310	0.81[ASN][1000 genomes]
rs336319	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336326	0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap]
rs336331	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs336332	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[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34087587	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775605	0.89[YRI][hapmap]
rs3775637	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4637485	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv830096	chr4:142867099-143023761	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv428775	chr4:142943213-143050195	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs336308	MAML3	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142948400-143029200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:142988200-143029400	Weak transcription	Left Ventricle	heart
3	chr4:142990000-143051200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:142997800-143024600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:143001400-143040600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:143002600-143041800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:143004000-143021800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:143004600-143051600	Weak transcription	Pancreas	Pancrea
9	chr4:143007400-143025400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:143007600-143024800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:143008000-143025600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:143010400-143043400	Weak transcription	Psoas Muscle	Psoas
13	chr4:143010400-143057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:143012400-143023000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr4:143012400-143040600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:143014000-143035800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr4:143014200-143021800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:143014400-143022600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:143014600-143026200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:143014600-143049600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:143015800-143027400	Weak transcription	Aorta	Aorta
22	chr4:143015800-143049600	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:143016000-143024600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:143016400-143024400	Strong transcription	Primary T cells from cord blood	blood
25	chr4:143016600-143030800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:143017600-143025400	Weak transcription	Dnd41	blood
27	chr4:143017800-143044400	Weak transcription	Fetal Heart	heart
28	chr4:143018000-143031000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:143018200-143021000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:143018200-143021200	Weak transcription	HSMMtube	muscle
31	chr4:143018200-143021400	Weak transcription	HUVEC	blood vessel
32	chr4:143018200-143022000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr4:143018200-143022400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:143018200-143029000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:143018200-143033400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:143018800-143029000	Weak transcription	NHEK	skin
37	chr4:143018800-143109600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr4:143019200-143023000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:143019200-143024200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:143019600-143022600	Weak transcription	A549	lung
41	chr4:143019600-143023200	Strong transcription	HSMM	muscle
42	chr4:143019800-143025800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:143019800-143026400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr4:143020000-143020800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:143020000-143021600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:143020200-143021200	Weak transcription	HMEC	breast
47	chr4:143020600-143022200	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links