Variant report

Variant	rs486370
Chromosome Location	chr1:93480191-93480192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93458381..93461372-chr1:93479810..93482559,2	MCF-7	breast:
2	chr1:93408180..93410654-chr1:93478958..93480924,2	K562	blood:
3	chr1:93297396..93299866-chr1:93478286..93480481,2	K562	blood:

Variant related genes	Relation type
ENSG00000122406	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11164860	0.96[ASN][1000 genomes]
rs11164861	0.99[ASN][1000 genomes]
rs12022729	0.95[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs12023767	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs12027025	0.87[ASN][1000 genomes]
rs12039256	0.87[ASN][1000 genomes]
rs12043007	0.87[CHB][hapmap]
rs12043577	0.95[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs12119421	0.86[ASN][1000 genomes]
rs12130551	0.99[ASN][1000 genomes]
rs12134501	0.87[ASN][1000 genomes]
rs12141895	0.87[ASN][1000 genomes]
rs1678778	0.87[ASN][1000 genomes]
rs2086312	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2253595	0.85[ASN][1000 genomes]
rs2492898	0.86[ASN][1000 genomes]
rs2928183	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626900	0.87[ASN][1000 genomes]
rs4847227	0.88[ASN][1000 genomes]
rs485336	0.87[ASN][1000 genomes]
rs492054	0.87[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs492754	0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs496465	0.87[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs497540	0.91[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs504418	0.87[ASN][1000 genomes]
rs517856	0.85[ASN][1000 genomes]
rs521527	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs524045	0.88[ASN][1000 genomes]
rs553396	0.84[ASN][1000 genomes]
rs557812	0.86[ASN][1000 genomes]
rs56320266	0.98[ASN][1000 genomes]
rs572131	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57478994	0.88[ASN][1000 genomes]
rs590296	0.87[ASN][1000 genomes]
rs591820	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs591868	0.97[ASN][1000 genomes]
rs592751	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs664524	0.85[ASN][1000 genomes]
rs664852	0.86[ASN][1000 genomes]
rs6674738	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs680285	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs808833	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9787147	0.95[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs486370	MTF2	cis	parietal	SCAN
rs486370	ARHGAP29	cis	parietal	SCAN
rs486370	GEMIN8P4	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93474200-93490600	Weak transcription	K562	blood
2	chr1:93478200-93481400	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr1:93478200-93481600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr1:93478200-93482600	Enhancers	Fetal Muscle Leg	muscle
5	chr1:93478800-93480200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:93478800-93480400	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr1:93478800-93480800	Enhancers	Psoas Muscle	Psoas
8	chr1:93478800-93482400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:93478800-93482400	Enhancers	HSMMtube	muscle
10	chr1:93479000-93480400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:93479000-93481400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:93479000-93482200	Enhancers	HSMM	muscle
13	chr1:93479200-93480200	Enhancers	Adipose Nuclei	Adipose
14	chr1:93479200-93480800	Weak transcription	NHDF-Ad	bronchial
15	chr1:93479200-93481400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:93479600-93480400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:93479600-93480400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:93479600-93480600	Flanking Active TSS	GM12878-XiMat	blood
19	chr1:93479600-93481000	Enhancers	Fetal Thymus	thymus
20	chr1:93479600-93481400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:93479600-93482200	Enhancers	HUVEC	blood vessel
22	chr1:93479800-93481800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:93480000-93480600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:93480000-93481000	Weak transcription	Hela-S3	cervix
25	chr1:93480000-93481400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:93480000-93481800	Weak transcription	HepG2	liver

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