Variant report

Variant	rs3775465
Chromosome Location	chr4:90827466-90827467
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10433954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10433955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10516851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10516852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10516853	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs11722543	0.88[ASN][1000 genomes]
rs12640573	1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs12640925	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12640973	0.85[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12641781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12643823	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12644375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646270	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1372511	0.89[ASN][1000 genomes]
rs1372512	0.89[ASN][1000 genomes]
rs1442131	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1442132	0.81[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs16996201	0.91[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs17016274	0.94[JPT][hapmap]
rs17016373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17016396	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs2241884	0.96[ASN][1000 genomes]
rs3775464	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs3775466	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs3775467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775473	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3775474	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775476	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3775477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56146644	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57925841	0.89[ASN][1000 genomes]
rs58514521	1.00[ASN][1000 genomes]
rs58930449	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59559279	0.87[ASN][1000 genomes]
rs60847430	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61160271	0.96[ASN][1000 genomes]
rs61611959	0.90[ASN][1000 genomes]
rs6532197	0.81[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6532199	0.89[ASN][1000 genomes]
rs6532200	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs67212195	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6828095	0.89[ASN][1000 genomes]
rs6837483	0.82[EUR][1000 genomes]
rs6838943	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6847403	0.89[ASN][1000 genomes]
rs6848022	0.89[ASN][1000 genomes]
rs6857668	0.95[ASN][1000 genomes]
rs6858182	0.98[ASN][1000 genomes]
rs72657800	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72657801	1.00[ASN][1000 genomes]
rs72657802	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72659403	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72659404	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72659409	0.98[ASN][1000 genomes]
rs72659413	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73831836	0.89[ASN][1000 genomes]
rs73831856	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7657014	0.83[ASN][1000 genomes]
rs7666981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673735	0.89[ASN][1000 genomes]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3775465	MMRN1	cis	parietal	SCAN
rs3775465	SLC10A6	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90820000-90827600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:90822800-90830600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:90823000-90830400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:90825400-90828400	Enhancers	HUVEC	blood vessel
5	chr4:90826000-90830400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:90826800-90835800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:90827000-90827600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:90827200-90828600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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