Variant report

Variant	rs2576270
Chromosome Location	chr1:217064958-217064959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1025651	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1025654	0.89[CEU][hapmap]
rs2576202	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818743	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818744	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147268	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4436447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688971	0.83[CEU][hapmap];0.89[JPT][hapmap]

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	nsv873179	chr1:217056893-217112871	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2576270	USH2A	cis	parietal	SCAN
rs2576270	ATF3	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217058200-217067600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:217058400-217065200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:217058400-217067800	Weak transcription	Small Intestine	intestine
4	chr1:217058600-217067800	Weak transcription	Fetal Kidney	kidney
5	chr1:217058800-217066000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:217062600-217067600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:217062600-217078000	Weak transcription	Pancreas	Pancrea
8	chr1:217062800-217065200	Weak transcription	Fetal Intestine Small	intestine
9	chr1:217062800-217066000	Weak transcription	Psoas Muscle	Psoas
10	chr1:217062800-217067400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:217062800-217068000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:217062800-217068000	Weak transcription	Left Ventricle	heart
13	chr1:217062800-217076000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:217062800-217076200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:217062800-217087800	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:217063000-217065600	Weak transcription	Fetal Intestine Large	intestine
17	chr1:217063000-217066200	Weak transcription	Fetal Heart	heart
18	chr1:217064000-217065600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:217064600-217065000	Bivalent Enhancer	Fetal Brain Male	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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