Variant report

Variant	rs2326613
Chromosome Location	chr6:5545046-5545047
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11243018	0.91[ASN][1000 genomes]
rs4499976	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs56227176	0.82[ASN][1000 genomes]
rs6926945	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6942094	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7749599	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs7751245	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7751261	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9405846	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv2763528	chr6:5539805-5545654	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
12	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2326613	GMDS	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5501000-5550600	Weak transcription	Pancreas	Pancrea
2	chr6:5508000-5547400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:5511200-5546400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:5511400-5568200	Weak transcription	Aorta	Aorta
5	chr6:5518600-5550000	Weak transcription	Right Ventricle	heart
6	chr6:5522600-5548000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:5522800-5550400	Weak transcription	GM12878-XiMat	blood
8	chr6:5523000-5549000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:5525200-5547600	Weak transcription	Primary B cells from cord blood	blood
10	chr6:5529000-5546800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:5531600-5546800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:5532400-5551600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:5532800-5550400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:5533000-5550400	Weak transcription	Psoas Muscle	Psoas
15	chr6:5536000-5550000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:5536800-5553000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:5538000-5550600	Weak transcription	Lung	lung
18	chr6:5538000-5573600	Weak transcription	Left Ventricle	heart
19	chr6:5538600-5550200	Weak transcription	Fetal Stomach	stomach
20	chr6:5538800-5550600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:5539000-5547800	Weak transcription	Small Intestine	intestine
22	chr6:5539000-5550000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:5539200-5545400	Weak transcription	Fetal Brain Male	brain
24	chr6:5540400-5550600	Weak transcription	Esophagus	oesophagus
25	chr6:5540800-5545400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr6:5541200-5550400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:5541600-5547200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:5542400-5547800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:5542400-5550000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:5542600-5545200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:5542600-5549000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:5542600-5549600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:5542600-5550800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:5542600-5555400	Weak transcription	Gastric	stomach
35	chr6:5542800-5545200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:5542800-5546600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:5542800-5547400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:5542800-5547800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:5542800-5551000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:5543000-5549400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:5543000-5549600	Weak transcription	Placenta	Placenta
42	chr6:5543400-5550600	Weak transcription	Thymus	Thymus
43	chr6:5543600-5547800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:5543600-5549400	Weak transcription	HMEC	breast
45	chr6:5543800-5545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:5544000-5550400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:5544000-5550600	Weak transcription	Dnd41	blood
48	chr6:5544200-5546600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:5544200-5550000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:5544400-5545400	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links