Variant report

Variant	rs6544331
Chromosome Location	chr2:40591189-40591190
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11678256	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11687700	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11886400	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11890040	0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12469017	0.83[ASN][1000 genomes]
rs12472012	0.82[JPT][hapmap]
rs12472064	0.85[ASN][1000 genomes]
rs12615002	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs17025877	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs34408472	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61578092	0.85[ASN][1000 genomes]
rs6724743	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72939976	0.97[ASN][1000 genomes]
rs72939984	0.93[ASN][1000 genomes]
rs7557545	0.83[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap]

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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873915	chr2:40573350-40615520	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6544331	KCNG3	cis	parietal	SCAN
rs6544331	ABCG8	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40581200-40591800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:40581600-40591600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr2:40586400-40592000	Weak transcription	Left Ventricle	heart
4	chr2:40586800-40593800	Enhancers	Fetal Heart	heart
5	chr2:40589600-40591800	Enhancers	Rectal Smooth Muscle	rectum
6	chr2:40590200-40592200	Active TSS	Stomach Smooth Muscle	stomach
7	chr2:40590400-40591600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr2:40590400-40591600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:40590400-40591800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:40590400-40592000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:40590400-40592400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr2:40590400-40592400	Active TSS	Right Atrium	heart
13	chr2:40590600-40591400	Enhancers	A549	lung
14	chr2:40590600-40591800	Enhancers	Brain Germinal Matrix	brain
15	chr2:40590600-40592200	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr2:40590600-40592400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:40590600-40592400	Active TSS	Aorta	Aorta
18	chr2:40590800-40591200	Enhancers	Brain Angular Gyrus	brain
19	chr2:40590800-40591200	Enhancers	HSMMtube	muscle
20	chr2:40590800-40591400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr2:40590800-40591400	Enhancers	HMEC	breast
22	chr2:40590800-40591600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:40590800-40591600	Active TSS	Psoas Muscle	Psoas
24	chr2:40591000-40591200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:40591000-40591200	Active TSS	NHDF-Ad	bronchial
26	chr2:40591000-40591400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:40591000-40591400	Flanking Active TSS	HUVEC	blood vessel
28	chr2:40591000-40591400	Enhancers	NH-A	brain
29	chr2:40591000-40591600	Weak transcription	Ovary	ovary
30	chr2:40591000-40591600	Weak transcription	HSMM	muscle
31	chr2:40591000-40591600	Flanking Active TSS	Osteobl	bone
32	chr2:40591000-40591800	Weak transcription	Primary B cells from cord blood	blood
33	chr2:40591000-40591800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:40591000-40591800	Active TSS	Brain Anterior Caudate	brain
35	chr2:40591000-40591800	Weak transcription	Fetal Brain Male	brain
36	chr2:40591000-40591800	Enhancers	Hela-S3	cervix
37	chr2:40591000-40592000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:40591000-40592000	Active TSS	Colon Smooth Muscle	Colon
39	chr2:40591000-40592000	Weak transcription	Fetal Brain Female	brain
40	chr2:40591000-40592000	Active TSS	Fetal Kidney	kidney
41	chr2:40591000-40592200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:40591000-40592200	Active TSS	Fetal Lung	lung
43	chr2:40591000-40592200	Active TSS	NHLF	lung
44	chr2:40591000-40598400	Weak transcription	Fetal Stomach	stomach

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