Variant report

Variant	rs17042407
Chromosome Location	chr2:113558914-113558915
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:19)

rs_ID	r²[population]
rs10169524	0.81[ASN][1000 genomes]
rs11680809	0.88[ASN][1000 genomes]
rs17598291	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2071374	0.82[ASN][1000 genomes]
rs2856838	0.81[ASN][1000 genomes]
rs3783515	0.81[ASN][1000 genomes]
rs3783516	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs3783547	0.81[ASN][1000 genomes]
rs4849123	0.80[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62157427	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157428	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157435	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6710316	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6716046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6746923	0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs7585707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17042407	ZC3H8	cis	parietal	SCAN
rs17042407	IL1B	cis	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113542400-113559200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:113543000-113562200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:113552800-113560800	Weak transcription	Osteobl	bone
4	chr2:113553600-113559000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:113553600-113559000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:113553600-113561200	Weak transcription	K562	blood
7	chr2:113553600-113562800	Weak transcription	Esophagus	oesophagus
8	chr2:113553800-113559200	Weak transcription	Hela-S3	cervix
9	chr2:113553800-113563000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:113555600-113563200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:113557400-113559000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:113557400-113560600	Weak transcription	HMEC	breast
13	chr2:113557400-113560600	Weak transcription	NHEK	skin
14	chr2:113558200-113559000	Enhancers	HepG2	liver
15	chr2:113558400-113559000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:113558600-113561400	Weak transcription	GM12878-XiMat	blood
17	chr2:113558800-113559400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:113558800-113559600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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

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