Variant report

Variant	rs1032398
Chromosome Location	chr3:111858474-111858475
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	chr3:111851024..111853542-chr3:111855899..111858560,2	K562	blood:

Variant related genes	Relation type
ENSG00000261488	Chromatin interaction
ENSG00000174500	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10934145	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs10934162	0.81[CHB][hapmap]
rs11707558	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11922559	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11923778	0.83[CHB][hapmap]
rs12488760	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12491362	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12634742	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs12634769	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12637609	1.00[CHB][hapmap]
rs13081485	1.00[CHB][hapmap]
rs13081935	0.83[CHB][hapmap]
rs13082509	0.83[CHB][hapmap]
rs13087086	0.83[CHB][hapmap]
rs13100724	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1492491	0.91[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs16859207	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16859355	0.83[AFR][1000 genomes]
rs17446744	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2120095	0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs340163	0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs340164	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4234412	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4234413	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4276157	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4282033	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4282034	0.87[ASW][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4300982	0.83[CHB][hapmap]
rs4392388	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4398404	0.81[CHB][hapmap]
rs4401342	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4450779	0.81[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4505669	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4560270	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4572740	0.83[CHB][hapmap]
rs4585166	0.83[CHB][hapmap]
rs4611789	0.83[CHB][hapmap]
rs4632517	0.83[CHB][hapmap]
rs4682097	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4682380	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs58167335	1.00[ASN][1000 genomes]
rs59043683	0.81[AFR][1000 genomes]
rs6773916	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs6781344	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs6791182	0.91[CHB][hapmap]
rs6798551	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs6798665	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7613061	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7616261	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7624367	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7627314	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7638520	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9758396	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9809384	0.83[CHB][hapmap]
rs9809404	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9822786	0.83[CHB][hapmap]
rs9823421	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9826043	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9847574	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs9860819	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9863061	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs9870132	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9878213	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9879184	0.82[CHB][hapmap];0.81[JPT][hapmap]

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	nsv1010219	chr3:111856709-111923647	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1032398	UPK1A	trans	parietal	SCAN
rs1032398	KIAA1407	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111852200-111863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:111853400-111867400	Weak transcription	Gastric	stomach
3	chr3:111856200-111860200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:111856200-111867400	Weak transcription	Thymus	Thymus
5	chr3:111856200-111867600	Weak transcription	Left Ventricle	heart
6	chr3:111856400-111861800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:111856400-111862400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:111857000-111861000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:111857200-111860200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:111858400-111858800	Enhancers	Primary T helper cells PMA-I stimulated	--

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