Variant report

Variant	rs7550628
Chromosome Location	chr1:222039315-222039316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10746414	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10863657	1.00[ASN][1000 genomes]
rs10863664	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11118874	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118875	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11118883	1.00[CHB][hapmap]
rs11577023	1.00[CHB][hapmap]
rs11579490	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582814	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12083393	1.00[ASN][1000 genomes]
rs12089785	1.00[ASN][1000 genomes]
rs12090948	1.00[ASN][1000 genomes]
rs12095068	1.00[ASN][1000 genomes]
rs12118052	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125690	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[ASN][1000 genomes]
rs12130910	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35090621	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4308986	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs4384245	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528124	0.88[CEU][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs4581289	1.00[ASN][1000 genomes]
rs56010022	1.00[ASN][1000 genomes]
rs6604675	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6604676	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6604677	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604678	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658977	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659311	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668784	1.00[ASN][1000 genomes]
rs66698149	1.00[ASN][1000 genomes]
rs6691170	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699132	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67087803	1.00[ASN][1000 genomes]
rs67220535	1.00[ASN][1000 genomes]
rs7544478	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7556214	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556228	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7550628	AIDA	cis	parietal	SCAN
rs7550628	CCDC137	trans	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222019800-222047600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:222032800-222041600	Weak transcription	NHEK	skin
3	chr1:222032800-222041800	Weak transcription	Osteobl	bone
4	chr1:222033200-222041600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:222037400-222039400	Weak transcription	Gastric	stomach
6	chr1:222038000-222040200	Enhancers	NHDF-Ad	bronchial
7	chr1:222038000-222040800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:222038000-222041800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:222038200-222039600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:222038400-222041000	Enhancers	HMEC	breast
11	chr1:222038600-222039400	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:222038600-222039400	Enhancers	Fetal Muscle Leg	muscle
13	chr1:222038600-222039600	Enhancers	NH-A	brain
14	chr1:222038600-222039600	Enhancers	NHLF	lung
15	chr1:222038600-222039800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:222038600-222040000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:222038600-222040200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:222038800-222040000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:222039000-222041600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:222039200-222039800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:222039200-222039800	Enhancers	HSMM	muscle

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