Variant report

Variant	rs669358
Chromosome Location	chr1:57404739-57404740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12116668	1.00[GIH][hapmap]
rs598772	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs605648	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623077	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs624298	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs635833	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs652553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706480	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs669358	BSND	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57395600-57410000	Strong transcription	Liver	Liver
2	chr1:57400800-57405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:57404400-57405200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:57404400-57405200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:57404400-57405600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr1:57404400-57405600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr1:57404600-57404800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
8	chr1:57404600-57405000	Enhancers	Fetal Brain Male	brain
9	chr1:57404600-57405000	Enhancers	Fetal Brain Female	brain
10	chr1:57404600-57405400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr1:57404600-57405400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr1:57404600-57405400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:57404600-57405400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:57404600-57405400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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Input of quick search could be:

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

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