Variant report

Variant	rs2875997
Chromosome Location	chr6:5550655-5550656
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	chr6:5549888..5552504-chr6:5555146..5558122,2	K562	blood:
2	chr6:5549888..5553907-chr6:5554178..5558122,4	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10484312	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12202010	0.85[ASN][1000 genomes]
rs9378428	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9405847	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription 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	10 gene(s)	inside rSNPs	diseases
3	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1017506	chr6:5443538-5551125	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv883420	chr6:5524393-5584422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv5181	chr6:5536921-5581595	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5511400-5568200	Weak transcription	Aorta	Aorta
2	chr6:5532400-5551600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr6:5536800-5553000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:5538000-5573600	Weak transcription	Left Ventricle	heart
5	chr6:5542600-5550800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:5542600-5555400	Weak transcription	Gastric	stomach
7	chr6:5542800-5551000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:5544800-5550800	Weak transcription	HepG2	liver
9	chr6:5545200-5556600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:5545400-5560000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:5546000-5550800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:5546200-5555800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr6:5549000-5551400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:5549600-5551600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr6:5550000-5550800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr6:5550000-5550800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:5550000-5551000	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr6:5550000-5551600	Strong transcription	Primary B cells from cord blood	blood
19	chr6:5550200-5550800	ZNF genes & repeats	Fetal Muscle Leg	muscle
20	chr6:5550200-5551000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr6:5550200-5551200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:5550200-5551600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr6:5550400-5550800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:5550400-5551000	ZNF genes & repeats	Primary T cells from cord blood	blood
25	chr6:5550400-5551000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr6:5550600-5550800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:5550600-5550800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
28	chr6:5550600-5550800	Enhancers	Esophagus	oesophagus
29	chr6:5550600-5550800	ZNF genes & repeats	Lung	lung
30	chr6:5550600-5550800	ZNF genes & repeats	Pancreas	Pancrea
31	chr6:5550600-5550800	ZNF genes & repeats	Thymus	Thymus
32	chr6:5550600-5550800	ZNF genes & repeats	Dnd41	blood
33	chr6:5550600-5551000	ZNF genes & repeats	Ovary	ovary
34	chr6:5550600-5551200	ZNF genes & repeats	Liver	Liver
35	chr6:5550600-5551400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:5550600-5551800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links