Variant report

Variant	rs594799
Chromosome Location	chr1:216317495-216317496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11120735	0.84[TSI][hapmap]
rs12091601	0.80[AFR][1000 genomes]
rs17597445	1.00[CHB][hapmap]
rs17649639	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1830857	1.00[CHD][hapmap]
rs2926178	1.00[CHB][hapmap]
rs301743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301745	0.83[LWK][hapmap]
rs301748	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs301749	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs301751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs301753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[TSI][hapmap]
rs301756	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs301757	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs301758	1.00[CHB][hapmap]
rs3106400	1.00[CHB][hapmap]
rs368107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371947	0.80[CEU][hapmap];0.89[AMR][1000 genomes]
rs386851	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[TSI][hapmap]
rs400358	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs403340	1.00[CHB][hapmap]
rs414373	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs446247	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs448588	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449118	1.00[CHB][hapmap]
rs452747	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs453273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471271	1.00[CHB][hapmap]
rs532342	1.00[CHD][hapmap];0.90[MEX][hapmap]
rs551895	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619803	0.86[ASN][1000 genomes]
rs637374	0.89[AMR][1000 genomes]
rs656949	1.00[CHB][hapmap]
rs658740	1.00[CHB][hapmap]
rs676212	1.00[CEU][hapmap]
rs682319	1.00[CHB][hapmap]
rs687476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413858	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs74141506	0.80[AFR][1000 genomes]
rs9729724	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv873176	chr1:216249570-216363137	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv999211	chr1:216268796-216329336	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1006028	chr1:216268796-216432545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs594799	PINX1	trans	parietal	SCAN
rs594799	TMEM206	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216314000-216317800	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr1:216314400-216318000	Weak transcription	Fetal Lung	lung
3	chr1:216315000-216318000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:216315000-216318200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:216315000-216324000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:216315200-216318000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:216316400-216318000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:216316400-216318000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr1:216316800-216317600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
10	chr1:216317200-216318400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:216317200-216318600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:216317400-216318400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr1:216317400-216318800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:216317400-216318800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:216317400-216319000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:216317400-216319000	Enhancers	HUES64 Cell Line	embryonic stem cell

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