Variant report

Variant	rs6812004
Chromosome Location	chr4:90877962-90877963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1046994	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516854	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11097241	0.82[EUR][1000 genomes]
rs11931134	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11931138	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940898	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13107488	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13109927	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13152356	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1443797	0.86[TSI][hapmap]
rs17201659	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35763285	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3775482	0.84[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3775483	0.84[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3899491	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626162	0.80[CHB][hapmap]
rs56073501	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837771	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6842029	0.81[TSI][hapmap]
rs755053	0.83[EUR][1000 genomes]
rs7686547	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs962542	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs964776	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs992731	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs993331	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv997700	chr4:90791866-90920021	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830005	chr4:90799398-90963420	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1003903	chr4:90831805-90947922	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1011876	chr4:90851535-90952723	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv998230	chr4:90854555-90952723	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv999030	chr4:90859531-90952723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv432616	chr4:90862943-90952424	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv516189	chr4:90866819-90952424	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv594821	chr4:90871561-90962886	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv1793223	chr4:90876066-90880889	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6812004	DSPP	cis	cerebellum	SCAN
rs6812004	SNCA	cis	cerebellum	SCAN
rs6812004	MMRN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90856800-90878200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:90872800-90878600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:90873800-90878200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:90874000-90878200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:90874000-90878400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:90874000-90878400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:90874200-90878200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:90875400-90878200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr4:90876600-90878200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:90876600-90878200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:90876800-90878200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:90876800-90878400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:90876800-90878600	Weak transcription	HUVEC	blood vessel
14	chr4:90876800-90882000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:90877800-90878400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:90877800-90878600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:90877800-90879200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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