Variant report

Variant	rs373300
Chromosome Location	chr2:39154463-39154464
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39139462..39141129-chr2:39152347..39155038,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1010858	0.90[AMR][1000 genomes]
rs1010859	0.81[MEX][hapmap];0.84[TSI][hapmap]
rs10173240	0.85[JPT][hapmap]
rs10181808	0.87[EUR][1000 genomes]
rs10204999	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10779923	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[ASN][1000 genomes]
rs11124654	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11124655	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11689954	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12617734	0.81[ASN][1000 genomes]
rs12621073	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12623330	0.86[JPT][hapmap]
rs12712621	0.93[JPT][hapmap]
rs12712625	0.86[ASW][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs12712626	0.83[YRI][hapmap]
rs12712627	0.86[ASW][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs12712628	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13029388	0.83[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs13029406	0.86[JPT][hapmap]
rs13383541	0.86[JPT][hapmap]
rs1530852	0.86[JPT][hapmap]
rs1530853	0.86[JPT][hapmap]
rs17422748	0.87[EUR][1000 genomes]
rs1868867	0.96[ASN][1000 genomes]
rs1901289	0.93[ASW][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs1979142	0.85[JPT][hapmap]
rs3099941	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs3099942	0.89[GIH][hapmap]
rs3099945	0.86[GIH][hapmap]
rs3099958	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs3099959	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs3770681	0.86[JPT][hapmap]
rs384007	0.84[EUR][1000 genomes]
rs384421	0.86[EUR][1000 genomes]
rs389023	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs390008	0.96[ASN][1000 genomes]
rs3923144	0.86[MEX][hapmap]
rs4265996	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[ASN][1000 genomes]
rs434696	0.85[EUR][1000 genomes]
rs4670267	0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs4670268	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs4670899	0.92[CEU][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6544180	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6706091	0.81[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706186	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6738069	0.81[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6744514	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7419616	0.86[JPT][hapmap]
rs7565111	0.86[JPT][hapmap]
rs7589162	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs7598922	0.86[ASW][hapmap];0.86[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs9808136	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs986019	0.85[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	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs373300	DHX57	cis	multi-tissue	Pritchard
rs373300	DHX57	cis	cerebellum	SCAN
rs373300	MORN2	cis	parietal	SCAN
rs373300	ITGB1	trans	parietal	SCAN
rs373300	DHX57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39110200-39186800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:39143800-39164600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:39145800-39172800	Weak transcription	Lung	lung
4	chr2:39147000-39166600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:39149000-39164800	Weak transcription	Ovary	ovary
6	chr2:39150000-39186600	Weak transcription	Brain Anterior Caudate	brain
7	chr2:39150400-39184800	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links