Variant report

Variant	rs2353315
Chromosome Location	chr4:48462902-48462903
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48461047..48463475-chr4:48463503..48465946,2	MCF-7	breast:
2	chr4:48462803..48464644-chr4:48465855..48467881,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10029785	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs1015699	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10805168	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10938534	0.81[JPT][hapmap]
rs1117010	0.90[ASN][1000 genomes]
rs11731383	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11737677	0.81[JPT][hapmap]
rs11945562	0.86[JPT][hapmap]
rs12503644	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12507206	0.91[ASN][1000 genomes]
rs12511991	0.91[ASN][1000 genomes]
rs12645501	0.81[JPT][hapmap]
rs12645951	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12649527	0.89[ASN][1000 genomes]
rs12649528	0.89[ASN][1000 genomes]
rs13105385	0.90[ASN][1000 genomes]
rs13115295	0.91[ASN][1000 genomes]
rs13119041	0.81[JPT][hapmap]
rs13133788	0.83[ASN][1000 genomes]
rs13148849	0.90[ASN][1000 genomes]
rs1352433	0.89[ASN][1000 genomes]
rs1352434	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1472967	1.00[JPT][hapmap]
rs1488647	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1507865	1.00[ASW][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs1586540	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17575720	0.81[JPT][hapmap]
rs17656094	0.81[JPT][hapmap]
rs1876469	0.81[JPT][hapmap]
rs1948167	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2029348	0.82[ASN][1000 genomes]
rs2291474	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2291475	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2353312	0.85[ASN][1000 genomes]
rs2353314	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2353855	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28409655	0.87[ASN][1000 genomes]
rs28470767	0.81[JPT][hapmap]
rs34975258	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35758434	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3828496	0.90[ASN][1000 genomes]
rs392187	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs404445	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs411261	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs421833	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4536901	1.00[ASW][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs4694895	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695377	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4695381	0.90[EUR][1000 genomes]
rs4695391	1.00[ASW][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs62309455	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62309458	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6447634	0.90[ASN][1000 genomes]
rs6447635	0.82[ASN][1000 genomes]
rs6811148	0.81[JPT][hapmap]
rs6816010	0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6816352	0.84[ASN][1000 genomes]
rs6821277	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6829705	0.81[ASN][1000 genomes]
rs6829716	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6834339	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6836010	0.82[ASN][1000 genomes]
rs6836632	0.86[JPT][hapmap]
rs6838613	0.90[ASN][1000 genomes]
rs6843340	0.81[JPT][hapmap]
rs6844211	0.82[ASN][1000 genomes]
rs6848073	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6848395	0.82[ASN][1000 genomes]
rs7438704	0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7438713	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7654770	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs7667288	0.81[JPT][hapmap]
rs7672892	0.89[ASN][1000 genomes]
rs7674269	0.88[ASN][1000 genomes]
rs7678164	0.83[ASN][1000 genomes]
rs7678379	0.86[JPT][hapmap]
rs7679210	0.81[JPT][hapmap]
rs7683398	0.81[JPT][hapmap]
rs7693461	0.81[JPT][hapmap]
rs7697851	0.86[JPT][hapmap]
rs776584	0.81[JPT][hapmap]
rs776591	0.81[JPT][hapmap]
rs796555	1.00[ASW][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs923372	0.90[ASN][1000 genomes]
rs923373	0.90[ASN][1000 genomes]
rs9291323	0.89[ASN][1000 genomes]
rs937888	1.00[ASW][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs937889	0.81[JPT][hapmap]
rs952289	0.81[JPT][hapmap]
rs974014	0.90[ASN][1000 genomes]
rs974015	0.90[ASN][1000 genomes]
rs974016	0.88[ASN][1000 genomes]
rs992423	0.86[JPT][hapmap]
rs9996532	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv1005268	chr4:48444307-48484389	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv537086	chr4:48444307-48484389	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2353315	TEC	cis	lymphoblastoid	seeQTL
rs2353315	COMMD8	cis	cerebellum	SCAN
rs2353315	OCIAD2	cis	cerebellum	SCAN
rs2353315	SLC10A4	cis	lung	GTEx
rs2353315	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48462600-48463400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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