Variant report

Variant	rs476466
Chromosome Location	chr1:57663923-57663924
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs155286	0.84[CHB][hapmap]
rs155295	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs155298	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs155303	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs155305	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs155309	0.88[GIH][hapmap]
rs264040	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480836	0.80[CEU][hapmap];1.00[MEX][hapmap]
rs483280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483412	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs498772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512773	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515477	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs539315	0.84[CEU][hapmap];1.00[MEX][hapmap]
rs561703	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs570988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573385	1.00[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	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	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
rs476466	C8A	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57647000-57670600	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57657400-57670200	Weak transcription	Fetal Intestine Large	intestine
3	chr1:57658400-57664200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:57661600-57664200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:57662000-57664000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:57662200-57664600	Weak transcription	Fetal Brain Female	brain
7	chr1:57662800-57665200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:57663200-57665400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:57663600-57664000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:57663600-57669800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:57663800-57664000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:57663800-57664200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:57663800-57664600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr1:57663800-57664600	Enhancers	Fetal Brain Male	brain
15	chr1:57663800-57664800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:57663800-57665000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:57663800-57665200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:57663800-57665200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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