Variant report

Variant	rs3738490
Chromosome Location	chr1:216998464-216998465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11117688	0.82[YRI][hapmap]
rs12086610	0.82[YRI][hapmap]
rs12139635	0.99[ASN][1000 genomes]
rs1339340	1.00[ASN][1000 genomes]
rs1339358	0.84[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1370143	0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs1542001	0.84[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs17044026	0.94[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.99[ASN][1000 genomes]
rs2576237	0.84[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2789719	1.00[ASN][1000 genomes]
rs2789726	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs2813668	0.87[EUR][1000 genomes]
rs2813672	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2813675	0.84[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs6686329	0.84[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs766158	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs766159	0.84[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];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	esv2762163	chr1:216982140-217015625	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
2	nsv519715	chr1:216998155-216998464	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3738490	GPATCH2	cis	parietal	SCAN
rs3738490	USH2A	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216989000-217005800	Weak transcription	Left Ventricle	heart
2	chr1:216989600-217000600	Weak transcription	Psoas Muscle	Psoas
3	chr1:216994600-217004000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:216994800-216998600	Weak transcription	Fetal Heart	heart
5	chr1:216996400-217000400	Enhancers	Fetal Intestine Small	intestine
6	chr1:216996400-217004400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:216997000-216999600	Enhancers	Fetal Intestine Large	intestine
8	chr1:216997800-216998600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr1:216997800-216999400	Enhancers	Duodenum Mucosa	Duodenum
10	chr1:216998000-216998600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:216998000-216998600	Bivalent Enhancer	Fetal Lung	lung
12	chr1:216998000-216999200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:216998000-216999200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:216998200-216998600	Enhancers	H9 Cell Line	embryonic stem cell
15	chr1:216998200-216998800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr1:216998400-216999000	Weak transcription	Small Intestine	intestine

Quick Search:

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

what's new

Quick links