Variant report

Variant	rs17552506
Chromosome Location	chr3:142362179-142362180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11927681	0.83[EUR][1000 genomes]
rs17554211	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes]
rs62276447	0.85[EUR][1000 genomes]
rs62278462	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62278478	0.89[EUR][1000 genomes]
rs62278483	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9872776	0.83[AFR][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	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17552506	ATP1B3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142343400-142366400	Weak transcription	Fetal Intestine Small	intestine
2	chr3:142348800-142364800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:142355400-142363600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:142355400-142364000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:142357000-142371400	Weak transcription	Aorta	Aorta
6	chr3:142357600-142365200	Weak transcription	Colonic Mucosa	Colon
7	chr3:142358600-142365600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:142360800-142371400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:142361200-142362400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:142361400-142362400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr3:142361600-142362200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:142361600-142362400	Enhancers	H9 Cell Line	embryonic stem cell
13	chr3:142361600-142362400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:142361600-142362400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:142361600-142362600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:142361600-142362600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:142361600-142363400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:142361800-142362200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:142362000-142363800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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