Variant report

Variant	rs11752509
Chromosome Location	chr6:71434296-71434297
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	chr6:71433663..71435218-chr6:71436969..71438504,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13196394	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13197338	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs13198627	0.82[EUR][1000 genomes]
rs13202113	1.00[EUR][1000 genomes]
rs13203355	0.97[EUR][1000 genomes]
rs13212771	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs17763077	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34336229	0.97[EUR][1000 genomes]
rs34519120	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35293093	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35528153	0.87[ASN][1000 genomes]
rs4706459	0.89[ASN][1000 genomes]
rs4707848	0.87[ASN][1000 genomes]
rs67594983	0.88[ASN][1000 genomes]
rs68097508	0.85[EUR][1000 genomes]
rs9354939	0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9354940	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9680	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][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	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11752509	COL19A1	cis	parietal	SCAN
rs11752509	B3GAT2	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71420000-71435200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr6:71420000-71436800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:71422000-71435200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:71425400-71442600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr6:71426200-71443800	Weak transcription	Lung	lung
6	chr6:71426200-71451000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:71426400-71443000	Weak transcription	Primary B cells from cord blood	blood
8	chr6:71427200-71435000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:71427200-71439600	Weak transcription	Pancreas	Pancrea
10	chr6:71427400-71442600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:71427400-71444200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:71427600-71442600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:71428000-71442600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr6:71428200-71476400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:71430200-71442400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:71430600-71439600	Weak transcription	Left Ventricle	heart
17	chr6:71432200-71434400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:71432800-71434400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:71432800-71435800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:71432800-71436000	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr6:71433200-71435200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:71433200-71435200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:71433400-71435200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:71433600-71435000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:71433600-71435200	Weak transcription	Small Intestine	intestine
26	chr6:71434000-71435800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr6:71434200-71434400	Enhancers	Primary T cells from cord blood	blood
28	chr6:71434200-71434400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr6:71434200-71435200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr6:71434200-71436400	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links