Variant report

Variant	rs10863542
Chromosome Location	chr1:220463977-220463978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10863543	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11118518	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11589736	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1983247	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1983248	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2089861	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2089862	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4846623	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs756245	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs879449	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs925446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220462600-220464600	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr1:220463400-220464000	Enhancers	H1 Cell Line	embryonic stem cell
3	chr1:220463400-220464000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr1:220463400-220464200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:220463600-220464200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:220463600-220464200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:220463600-220465400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:220463800-220464000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:220463800-220464000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:220463800-220464200	Flanking Active TSS	HUES48 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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