Variant report

Variant	rs3765253
Chromosome Location	chr6:11717573-11717574
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11717459..11719677-chr6:11722650..11725386,2	MCF-7	breast:
2	chr6:11716333..11720276-chr6:11720959..11723559,3	K562	blood:
3	chr6:11717348..11719875-chr6:11747463..11750048,2	MCF-7	breast:
4	chr6:11715212..11717961-chr6:11734201..11736485,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEDD9-2	chr6:11717542-11717647	NONHSAT107762

Variant related genes	Relation type
ENSG00000111863	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs105924	0.98[ASN][1000 genomes]
rs12665068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs210896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs210897	0.98[ASN][1000 genomes]
rs210903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2235404	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2235417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2235421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294429	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711401	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713873	0.84[JPT][hapmap]
rs7747449	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9296142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9469927	0.82[AMR][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	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv428470	chr6:11686198-11747850	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462637	chr6:11710554-11733777	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv600990	chr6:11710554-11733777	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11710800-11731000	Weak transcription	Gastric	stomach
2	chr6:11711200-11731000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:11711400-11718400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:11711400-11719200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:11711600-11731800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:11712200-11718400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:11712400-11721000	Weak transcription	HSMM	muscle
8	chr6:11713200-11721000	Weak transcription	HMEC	breast
9	chr6:11713400-11723000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:11713400-11724600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:11713600-11718400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:11713600-11718600	Weak transcription	NHLF	lung
13	chr6:11713600-11727600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:11713800-11723200	Weak transcription	HSMMtube	muscle
15	chr6:11714000-11719200	Weak transcription	NHEK	skin
16	chr6:11714600-11731600	Weak transcription	Small Intestine	intestine
17	chr6:11715000-11718200	Weak transcription	Colonic Mucosa	Colon
18	chr6:11715200-11728000	Weak transcription	Fetal Thymus	thymus
19	chr6:11715800-11718400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:11715800-11723000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:11716000-11719000	Weak transcription	Primary T cells from cord blood	blood
22	chr6:11716000-11719000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr6:11716000-11719000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:11716400-11721600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:11716400-11721600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:11716400-11723000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:11716600-11723000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:11716800-11717600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:11716800-11718200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:11716800-11718600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:11716800-11721000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:11717000-11720000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:11717200-11722600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr6:11717400-11717600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:11717400-11719000	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links