Variant report

Variant	rs10496076
Chromosome Location	chr2:57942987-57942988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10186791	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10195687	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10196378	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10204616	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1040224	0.82[CEU][hapmap]
rs1040225	0.82[CEU][hapmap]
rs10496078	0.80[AMR][1000 genomes]
rs13402331	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13418015	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290867	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2678901	0.82[CEU][hapmap]
rs2678903	0.82[CEU][hapmap]
rs2678905	0.82[CEU][hapmap]
rs2678906	0.82[CEU][hapmap]
rs2678908	0.82[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs2717001	0.82[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs2717002	0.82[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs3886275	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6720888	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv874193	chr2:57758608-58066673	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1006688	chr2:57822953-58030203	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	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
rs10496076	CHAC2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:57938400-57947800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:57938400-57952400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:57938600-57945000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:57939600-57944800	Weak transcription	Fetal Thymus	thymus
5	chr2:57939600-57947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:57939600-57947800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:57939800-57945000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:57939800-57948200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:57941600-57944800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:57941800-57948200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:57942600-57943400	Enhancers	Brain Germinal Matrix	brain

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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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