Variant report

Variant	rs6544323
Chromosome Location	chr2:40582014-40582015
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10165271	0.91[ASN][1000 genomes]
rs10168748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs10178405	0.86[CHB][hapmap]
rs10192546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11124739	0.88[ASN][1000 genomes]
rs11690171	0.81[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12468092	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12712692	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12987979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs12988856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs12989200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs12989852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs12995004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[ASN][1000 genomes]
rs13014950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs13017968	0.81[CHB][hapmap]
rs13022231	0.85[CHB][hapmap]
rs13031340	0.81[CHB][hapmap]
rs13031441	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs13405065	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1477004	0.86[CHB][hapmap]
rs1558654	0.98[ASN][1000 genomes]
rs1558655	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[ASN][1000 genomes]
rs2373857	0.85[CHB][hapmap]
rs34443271	0.81[ASN][1000 genomes]
rs4446101	0.90[CHB][hapmap]
rs4645043	0.86[CHB][hapmap]
rs4952409	0.80[CHB][hapmap]
rs6544324	0.83[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6544325	0.98[ASN][1000 genomes]
rs6544326	0.98[ASN][1000 genomes]
rs6544329	0.97[ASN][1000 genomes]
rs6544330	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6544334	0.81[CHB][hapmap]
rs6709574	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6738580	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6738673	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7594786	0.80[ASN][1000 genomes]
rs967351	0.80[CHB][hapmap]
rs981739	0.86[CHB][hapmap]
rs984707	0.81[CHB][hapmap]
rs990270	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1010508	chr2:40526981-40590777	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv535655	chr2:40526981-40590777	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv873914	chr2:40573350-40586022	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6544323	SOS1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40552800-40590600	Weak transcription	Fetal Kidney	kidney
2	chr2:40571600-40582600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:40574600-40586000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:40574600-40590600	Weak transcription	Aorta	Aorta
5	chr2:40576800-40587600	Weak transcription	NH-A	brain
6	chr2:40578400-40583400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:40578600-40583000	Enhancers	Fetal Heart	heart
8	chr2:40579400-40582400	Enhancers	Rectal Smooth Muscle	rectum
9	chr2:40579600-40586800	Enhancers	Colon Smooth Muscle	Colon
10	chr2:40580200-40583000	Weak transcription	Right Ventricle	heart
11	chr2:40580200-40583200	Enhancers	Hela-S3	cervix
12	chr2:40580200-40587600	Weak transcription	NHLF	lung
13	chr2:40580600-40584800	Weak transcription	Osteobl	bone
14	chr2:40580600-40586800	Weak transcription	NHDF-Ad	bronchial
15	chr2:40580600-40587600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:40580600-40587800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:40580600-40587800	Weak transcription	HMEC	breast
18	chr2:40581000-40582400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:40581200-40587600	Weak transcription	HSMM	muscle
20	chr2:40581200-40590400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:40581200-40591800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:40581600-40583200	Enhancers	Stomach Smooth Muscle	stomach
23	chr2:40581600-40591600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr2:40581800-40582600	Weak transcription	Right Atrium	heart
25	chr2:40581800-40582800	Weak transcription	Left Ventricle	heart
26	chr2:40582000-40582400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:40582000-40586000	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links