Variant report

Variant	rs4562685
Chromosome Location	chr1:212063323-212063324
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10863929	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11119807	0.83[ASN][1000 genomes]
rs11119813	0.91[ASN][1000 genomes]
rs11487823	0.91[ASN][1000 genomes]
rs12059988	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12076991	0.91[ASN][1000 genomes]
rs12077561	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12084756	0.83[ASN][1000 genomes]
rs12085235	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12085288	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12088743	0.83[ASN][1000 genomes]
rs12090490	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12095938	0.83[ASN][1000 genomes]
rs12410970	0.83[ASN][1000 genomes]
rs28768080	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28800280	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28862981	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3738197	0.91[ASN][1000 genomes]
rs3862952	0.83[ASN][1000 genomes]
rs4447046	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4537651	0.92[ASN][1000 genomes]
rs4623773	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56132364	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828259	0.83[ASN][1000 genomes]
rs61828491	0.91[ASN][1000 genomes]
rs61828492	0.86[ASN][1000 genomes]
rs61828510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540709	0.91[ASN][1000 genomes]
rs6662067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664082	0.83[ASN][1000 genomes]
rs6678582	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6684049	0.83[ASN][1000 genomes]
rs6704043	0.83[ASN][1000 genomes]
rs7518896	0.91[ASN][1000 genomes]
rs7524009	0.83[ASN][1000 genomes]
rs7534335	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	esv2762218	chr1:212046447-212087682	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4562685	INTS7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212060000-212068600	Weak transcription	A549	lung
2	chr1:212061600-212063600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:212061800-212064400	Weak transcription	Liver	Liver
4	chr1:212061800-212065600	Weak transcription	Adipose Nuclei	Adipose
5	chr1:212062000-212064000	Weak transcription	HepG2	liver
6	chr1:212062400-212063400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:212062400-212063400	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:212062400-212063600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:212062600-212063400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:212062600-212063400	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:212062600-212063400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:212062800-212063400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr1:212062800-212063400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:212063200-212064200	Weak transcription	Fetal Intestine Small	intestine
15	chr1:212063200-212065400	Weak transcription	Pancreas	Pancrea
16	chr1:212063200-212068600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:212063200-212070200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:212063200-212070200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:212063200-212074600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links