Variant report

Variant	rs6828371
Chromosome Location	chr4:15757601-15757602
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	chr4:15642778..15644328-chr4:15756806..15758696,2	MCF-7	breast:
2	chr4:15756091..15759053-chr4:15760303..15762164,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1004124	1.00[CEU][hapmap]
rs1112243	1.00[CEU][hapmap]
rs1112244	1.00[CEU][hapmap]
rs11574928	1.00[CEU][hapmap]
rs12500744	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12502292	0.80[EUR][1000 genomes]
rs16892370	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16892390	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16892438	1.00[CEU][hapmap]
rs16892441	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs16892453	1.00[CEU][hapmap]
rs1800051	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs2286552	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs2286553	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs3756243	1.00[CEU][hapmap]
rs3796865	1.00[CEU][hapmap]
rs3796866	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs3822256	1.00[CEU][hapmap]
rs3822257	1.00[CEU][hapmap]
rs4464559	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58156049	0.82[AMR][1000 genomes]
rs6822515	0.87[JPT][hapmap]
rs6837105	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7690685	1.00[CEU][hapmap]
rs884473	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs953870	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6828371	NINL	trans	brain	seeQTL
rs6828371	GRM4	trans	brain	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15752600-15767600	Weak transcription	Fetal Intestine Small	intestine
2	chr4:15755000-15757800	Enhancers	Primary T cells fromperipheralblood	blood
3	chr4:15755000-15757800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:15755000-15758400	Enhancers	HUVEC	blood vessel
5	chr4:15755200-15757800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr4:15755200-15757800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr4:15755200-15757800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr4:15755200-15757800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr4:15755400-15757800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr4:15755400-15757800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:15755600-15757800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:15755600-15759000	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr4:15755600-15760400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:15755800-15758000	Enhancers	Primary B cells from peripheral blood	blood
15	chr4:15755800-15759200	Flanking Active TSS	Dnd41	blood
16	chr4:15756200-15757800	Weak transcription	Spleen	Spleen
17	chr4:15757000-15758600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:15757200-15757800	Active TSS	Fetal Thymus	thymus
19	chr4:15757200-15757800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr4:15757200-15757800	Enhancers	Osteobl	bone
21	chr4:15757200-15758000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:15757200-15758200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:15757200-15758200	Enhancers	Hela-S3	cervix
24	chr4:15757200-15758400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr4:15757200-15758800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:15757200-15759000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr4:15757200-15759000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:15757200-15759000	Enhancers	NH-A	brain
29	chr4:15757200-15759200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr4:15757400-15757800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr4:15757400-15758000	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr4:15757400-15758000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:15757400-15758600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:15757400-15758800	Active TSS	Thymus	Thymus
35	chr4:15757400-15758800	Enhancers	HMEC	breast
36	chr4:15757400-15759200	Flanking Active TSS	GM12878-XiMat	blood
37	chr4:15757600-15757800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:15757600-15758600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr4:15757600-15758800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr4:15757600-15759000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:15757600-15759200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr4:15757600-15759200	Enhancers	Primary neutrophils fromperipheralblood	blood

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