Variant report

Variant	rs9861474
Chromosome Location	chr3:116070478-116070479
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:116068430..116070631-chr3:116074599..116076825,2	K562	blood:
2	chr3:116065365..116068537-chr3:116070392..116072433,3	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10212415	0.86[ASN][1000 genomes]
rs10212559	0.86[ASN][1000 genomes]
rs1030577	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11924642	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11928524	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12695326	1.00[ASN][1000 genomes]
rs13068349	0.97[ASN][1000 genomes]
rs13069948	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs13070962	0.88[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs13073414	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13077694	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13079395	0.90[JPT][hapmap]
rs13088599	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13323946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1367770	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1583183	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16824787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1731596	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs17647031	0.90[JPT][hapmap]
rs17647091	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17703257	0.90[JPT][hapmap]
rs1920183	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2033406	0.83[JPT][hapmap]
rs2867100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs34642483	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35061171	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4271908	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4831096	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs4831131	0.83[JPT][hapmap]
rs4831133	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4831134	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4831136	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4831138	0.86[ASN][1000 genomes]
rs6438315	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6775240	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786130	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs71323440	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71625206	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7619907	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7629472	0.87[ASN][1000 genomes]
rs7630011	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7634137	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7637573	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs7652554	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7652923	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9289050	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9289051	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9823016	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9823782	0.83[JPT][hapmap]
rs9827984	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9833356	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838534	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.87[ASN][1000 genomes]
rs9860105	0.86[ASN][1000 genomes]
rs9860236	0.89[ASN][1000 genomes]
rs9860260	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9870357	0.83[JPT][hapmap]
rs9989972	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9990359	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv877361	chr3:116017931-116138039	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9861474	RNF152	trans	lymphoblastoid	RTeQTL
rs9861474	LSAMP	cis	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116069000-116071000	Enhancers	Brain Substantia Nigra	brain
2	chr3:116069800-116071000	Weak transcription	Brain Angular Gyrus	brain
3	chr3:116070000-116071400	Enhancers	Rectal Smooth Muscle	rectum
4	chr3:116070200-116071000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:116070400-116071400	Enhancers	Colon Smooth Muscle	Colon

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