Variant report

Variant	rs7643426
Chromosome Location	chr3:46040267-46040268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46035715..46038580-chr3:46039426..46042867,3	MCF-7	breast:
2	chr3:46038853..46042411-chr3:46045896..46048992,3	K562	blood:

Variant related genes	Relation type
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11130080	0.85[CHB][hapmap]
rs12054287	0.94[CEU][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12635657	0.84[CHB][hapmap]
rs12639598	0.81[CHB][hapmap]
rs13060901	0.85[CHB][hapmap]
rs13073861	0.81[CHB][hapmap]
rs1392290	0.85[CHB][hapmap]
rs1491960	0.84[CEU][hapmap]
rs17078449	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs2131091	0.81[CHB][hapmap]
rs2133662	0.86[EUR][1000 genomes]
rs2373154	0.81[CHB][hapmap]
rs3774638	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs3796376	0.94[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3821883	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851347	0.85[CHB][hapmap]
rs4447807	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4490402	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs4683169	0.83[EUR][1000 genomes]
rs4683174	0.80[EUR][1000 genomes]
rs56800498	0.83[EUR][1000 genomes]
rs59767267	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60539039	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60991632	0.83[EUR][1000 genomes]
rs61254379	0.80[EUR][1000 genomes]
rs62242788	0.84[AMR][1000 genomes]
rs62242832	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62242846	0.83[EUR][1000 genomes]
rs62243869	0.80[EUR][1000 genomes]
rs62243875	0.86[EUR][1000 genomes]
rs62243876	0.86[EUR][1000 genomes]
rs62243906	0.82[EUR][1000 genomes]
rs62245106	0.84[AMR][1000 genomes]
rs6763341	0.86[EUR][1000 genomes]
rs6764042	0.85[CHB][hapmap]
rs6780163	0.85[CHB][hapmap]
rs6781121	0.84[JPT][hapmap]
rs6781668	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6800954	0.83[CEU][hapmap]
rs6807854	0.84[EUR][1000 genomes]
rs730983	0.84[CHB][hapmap]
rs737452	0.85[CHB][hapmap]
rs7623460	0.85[CHB][hapmap]
rs7629999	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936939	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs9818635	0.81[EUR][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7643426	ANO10	cis	parietal	SCAN
rs7643426	PRSS50	cis	lymphoblastoid	seeQTL
rs7643426	ABHD5	cis	cerebellum	SCAN
rs7643426	RHOA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46037600-46053000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:46037600-46064600	Weak transcription	Gastric	stomach
3	chr3:46038000-46041800	Weak transcription	Brain Substantia Nigra	brain
4	chr3:46038200-46041800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:46038200-46041800	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:46038200-46041800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:46038200-46042200	Weak transcription	Brain Angular Gyrus	brain
8	chr3:46038200-46047400	Weak transcription	Psoas Muscle	Psoas
9	chr3:46040200-46041400	Enhancers	Fetal Thymus	thymus

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