Variant report

Variant	rs17411375
Chromosome Location	chr3:47395135-47395136
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	chr3:47393587..47395849-chr3:48200453..48202910,2	K562	blood:
2	chr3:47391054..47393268-chr3:47394220..47396168,2	K562	blood:

Variant related genes	Relation type
ENSG00000235627	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1038394	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs1076394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs10865946	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs11130123	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs11130124	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs11130126	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs11130127	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130128	0.96[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes]
rs11130129	0.96[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs11130137	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs11705957	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11710013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs11710121	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs11710322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs11711265	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs11711824	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs11712445	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs11716763	0.96[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap]
rs11719877	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs11915074	0.92[CEU][hapmap]
rs11920853	0.92[CEU][hapmap]
rs11925823	0.88[EUR][1000 genomes]
rs11927371	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12486969	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12487736	0.83[EUR][1000 genomes]
rs12495169	0.85[JPT][hapmap]
rs12497225	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12632132	0.81[EUR][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13059519	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs13064843	0.88[EUR][1000 genomes]
rs13075233	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs13079098	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13094438	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs1531875	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1638676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs17080872	0.81[JPT][hapmap]
rs17410853	0.86[ASW][hapmap];0.85[CEU][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17784882	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap]
rs1872164	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2062278	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2101247	0.92[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes]
rs2132173	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs2159400	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276853	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs2276854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs2291298	0.96[CEU][hapmap]
rs295428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs295442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs295449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736177	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3816779	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs4241548	0.81[EUR][1000 genomes]
rs4683326	1.00[CEU][hapmap]
rs4858805	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4858811	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4858824	0.96[CEU][hapmap]
rs4858848	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858868	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs4858888	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858890	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858893	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4858894	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs553989	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56032309	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56351005	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57346147	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60369822	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62246474	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62248580	0.81[EUR][1000 genomes]
rs6768221	0.92[CEU][hapmap]
rs6780013	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs6787422	0.88[EUR][1000 genomes]
rs6791842	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs6792461	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6792488	0.80[EUR][1000 genomes]
rs6800271	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7613282	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641010	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs807810	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807931	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs807932	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs807936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs811115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs8180040	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878659	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs922957	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9683033	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17411375	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs17411375	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs17411375	C3orf75	cis	cerebellum	SCAN
rs17411375	PRKAR2A	cis	cerebellum	SCAN
rs17411375	CCDC12	cis	cerebellum	SCAN
rs17411375	AMIGO3	cis	cerebellum	SCAN
rs17411375	HYAL2	cis	cerebellum	SCAN
rs17411375	SCAP	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47386200-47395600	Weak transcription	Ovary	ovary
2	chr3:47386800-47400800	Weak transcription	Pancreas	Pancrea
3	chr3:47387600-47397200	Weak transcription	Lung	lung
4	chr3:47388000-47397200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:47388000-47400600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:47389400-47395800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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