Variant report

Variant	rs2517601
Chromosome Location	chr6:30074072-30074073
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11158	0.82[EUR][1000 genomes]
rs1264705	0.87[EUR][1000 genomes]
rs1264706	0.87[EUR][1000 genomes]
rs1573296	0.84[EUR][1000 genomes]
rs1970	0.84[EUR][1000 genomes]
rs2023473	0.90[EUR][1000 genomes]
rs2106072	0.82[EUR][1000 genomes]
rs2157678	0.84[EUR][1000 genomes]
rs2517622	0.82[EUR][1000 genomes]
rs2523729	0.82[EUR][1000 genomes]
rs2523978	0.90[EUR][1000 genomes]
rs2844789	0.87[EUR][1000 genomes]
rs3115631	0.82[EUR][1000 genomes]
rs8321	0.85[EUR][1000 genomes]
rs9261290	0.84[EUR][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	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2517601	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs2517601	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2517601	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2517601	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30070000-30075400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:30071600-30079200	Weak transcription	Gastric	stomach
3	chr6:30071800-30074800	Weak transcription	Spleen	Spleen
4	chr6:30072200-30078000	Weak transcription	Colonic Mucosa	Colon
5	chr6:30073200-30075200	Weak transcription	Hela-S3	cervix
6	chr6:30073400-30074200	Enhancers	HMEC	breast
7	chr6:30073600-30075800	Strong transcription	Fetal Intestine Small	intestine
8	chr6:30073800-30074200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:30074000-30074400	Enhancers	Stomach Mucosa	stomach

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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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