Variant report

Variant	rs4894196
Chromosome Location	chr2:177622704-177622705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1533302	0.85[ASN][1000 genomes]
rs3731797	0.89[JPT][hapmap]
rs6705679	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs6714936	0.85[CHB][hapmap];0.90[CHD][hapmap]

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	nsv527737	chr2:177538266-177692572	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv583686	chr2:177538266-177692572	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006500	chr2:177548521-177707097	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4894196	LOC100130691	cis	parietal	SCAN
rs4894196	ITGA6	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177614200-177622800	Weak transcription	Fetal Lung	lung
2	chr2:177616600-177627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:177616800-177627000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr2:177621200-177626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:177621200-177627000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:177621400-177626200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:177621400-177627200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:177622400-177622800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:177622400-177623000	Enhancers	Pancreas	Pancrea
10	chr2:177622600-177622800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:177622600-177623000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr2:177622600-177623200	Enhancers	Fetal Stomach	stomach
13	chr2:177622600-177623400	Enhancers	Right Atrium	heart
14	chr2:177622600-177628600	Weak transcription	iPS DF 6.9 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