Variant report

Variant	rs13215865
Chromosome Location	chr6:56753730-56753731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1044670	1.00[ASW][hapmap];0.83[GIH][hapmap]
rs13190784	0.81[TSI][hapmap]
rs13193465	1.00[GIH][hapmap]
rs13195825	0.93[AFR][1000 genomes]
rs13198484	0.93[AFR][1000 genomes]
rs13203600	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13205022	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13207768	1.00[ASW][hapmap]
rs13209099	0.93[AFR][1000 genomes]
rs13214032	1.00[AFR][1000 genomes]
rs13216793	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13220510	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13220575	1.00[GIH][hapmap]
rs1451707	0.86[AFR][1000 genomes]
rs1451708	0.86[AFR][1000 genomes]
rs1460561	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1599280	1.00[ASW][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1599281	0.81[EUR][1000 genomes]
rs17450853	0.81[EUR][1000 genomes]
rs17685045	0.81[AMR][1000 genomes]
rs17685143	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17685185	0.81[EUR][1000 genomes]
rs17685277	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[AFR][1000 genomes]
rs17685338	1.00[AFR][1000 genomes]
rs17685380	1.00[AFR][1000 genomes]
rs17752412	0.81[EUR][1000 genomes]
rs17752435	0.81[EUR][1000 genomes]
rs17752459	0.81[EUR][1000 genomes]
rs1903330	0.85[CEU][hapmap];1.00[LWK][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2817573	1.00[GIH][hapmap]
rs28360537	1.00[AFR][1000 genomes]
rs28360538	1.00[AFR][1000 genomes]
rs34009699	1.00[AFR][1000 genomes]
rs34027274	1.00[AFR][1000 genomes]
rs34232358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34259328	0.82[EUR][1000 genomes]
rs34399458	1.00[AFR][1000 genomes]
rs34616943	1.00[AFR][1000 genomes]
rs34714091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34733863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34752771	0.81[EUR][1000 genomes]
rs34812189	0.86[AFR][1000 genomes]
rs35202312	0.81[EUR][1000 genomes]
rs35434542	0.86[AFR][1000 genomes]
rs35527216	0.81[EUR][1000 genomes]
rs35860642	0.82[EUR][1000 genomes]
rs35961728	0.86[AFR][1000 genomes]
rs36112505	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3957366	1.00[ASW][hapmap]
rs4490669	0.81[EUR][1000 genomes]
rs55786720	0.82[EUR][1000 genomes]
rs56030203	0.81[EUR][1000 genomes]
rs58338781	0.82[EUR][1000 genomes]
rs61340009	0.81[EUR][1000 genomes]
rs6901944	1.00[GIH][hapmap]
rs71550519	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71564866	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71564868	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs720884	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[AFR][1000 genomes]
rs748996	0.81[EUR][1000 genomes]
rs7744799	0.85[CEU][hapmap]
rs7760385	1.00[AFR][1000 genomes]
rs9475752	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv508408	chr6:56735681-56773285	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv5315	chr6:56752042-56798761	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13215865	BEND6	cis	parietal	SCAN
rs13215865	DST	cis	cerebellum	SCAN
rs13215865	BEND6	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56734200-56755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:56734600-56755400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:56734800-56754200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:56734800-56754400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:56736400-56755800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:56741200-56754600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:56741600-56754200	Weak transcription	NHLF	lung
8	chr6:56743600-56753800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:56749200-56769600	Weak transcription	Brain Angular Gyrus	brain
10	chr6:56750600-56754400	Weak transcription	Osteobl	bone
11	chr6:56750800-56754600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:56751000-56754600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:56751200-56753800	Weak transcription	NHDF-Ad	bronchial
14	chr6:56752000-56754800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:56752200-56754800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:56752200-56754800	Weak transcription	HSMM	muscle
17	chr6:56752400-56767000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:56752600-56754200	Weak transcription	HSMMtube	muscle
19	chr6:56752600-56754400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr6:56752600-56755000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:56752800-56754600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:56753000-56754600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:56753000-56755600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:56753200-56753800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:56753200-56753800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr6:56753200-56753800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:56753200-56753800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:56753200-56755000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:56753200-56756200	Enhancers	HUVEC	blood vessel
30	chr6:56753400-56754200	Enhancers	A549	lung
31	chr6:56753400-56754200	Enhancers	GM12878-XiMat	blood
32	chr6:56753600-56753800	Enhancers	K562	blood
33	chr6:56753600-56754000	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr6:56753600-56754000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr6:56753600-56754200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:56753600-56754600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:56753600-56757600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:56753600-56769600	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links