Variant report

Variant	rs10873708
Chromosome Location	chr1:86067742-86067743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1116746	0.81[CHD][hapmap]
rs12120700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2389969	0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3753793	0.82[CEU][hapmap]
rs3753795	0.82[CEU][hapmap]
rs4370804	0.81[CHD][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap]
rs4949896	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4949911	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4949912	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4949914	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10873708	CLCA2	cis	cerebellum	SCAN
rs10873708	C1orf180	cis	cerebellum	SCAN
rs10873708	SSX2IP	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048800-86081200	Weak transcription	Gastric	stomach
2	chr1:86049000-86068400	Weak transcription	Psoas Muscle	Psoas
3	chr1:86053800-86071400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:86063000-86069400	Weak transcription	Fetal Lung	lung
5	chr1:86063600-86068000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:86064000-86072600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:86065000-86071600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:86065200-86067800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:86065200-86071400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:86065200-86072000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:86065600-86068200	Weak transcription	Fetal Stomach	stomach
12	chr1:86065800-86069000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:86066000-86068600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:86066600-86077000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:86067200-86068400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:86067600-86068400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:86067600-86069000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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