Variant report

Variant	rs9403725
Chromosome Location	chr6:145897622-145897623
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1011597	0.95[JPT][hapmap]
rs1070518	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11155438	0.95[JPT][hapmap]
rs12205752	0.81[ASN][1000 genomes]
rs12208812	0.81[ASN][1000 genomes]
rs1280275	0.81[ASN][1000 genomes]
rs1280276	0.81[ASN][1000 genomes]
rs1280279	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1292333	0.95[JPT][hapmap]
rs1292334	0.95[JPT][hapmap]
rs1337839	0.81[JPT][hapmap]
rs1337841	0.95[JPT][hapmap]
rs1415744	0.95[JPT][hapmap]
rs1415746	0.95[JPT][hapmap]
rs1415747	0.95[JPT][hapmap]
rs1890170	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1890171	0.95[JPT][hapmap]
rs2064185	0.94[JPT][hapmap]
rs2092295	0.81[ASN][1000 genomes]
rs2092297	0.81[ASN][1000 genomes]
rs2103633	0.81[ASN][1000 genomes]
rs2142978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2142980	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2206142	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2223411	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2235481	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs365747	0.81[ASN][1000 genomes]
rs365869	0.81[ASN][1000 genomes]
rs367065	0.81[ASN][1000 genomes]
rs367693	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs370654	0.81[ASN][1000 genomes]
rs383841	0.81[ASN][1000 genomes]
rs392612	0.81[ASN][1000 genomes]
rs399502	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs400329	0.81[ASN][1000 genomes]
rs403345	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs403956	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs408443	0.81[ASN][1000 genomes]
rs411785	0.81[ASN][1000 genomes]
rs414600	0.81[ASN][1000 genomes]
rs418701	0.81[ASN][1000 genomes]
rs426371	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427128	0.81[ASN][1000 genomes]
rs4335004	0.81[ASN][1000 genomes]
rs435671	0.81[ASN][1000 genomes]
rs436156	0.81[ASN][1000 genomes]
rs436498	0.81[ASN][1000 genomes]
rs4398765	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs441982	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs443628	0.81[ASN][1000 genomes]
rs446362	0.81[ASN][1000 genomes]
rs448258	0.81[ASN][1000 genomes]
rs450921	0.81[ASN][1000 genomes]
rs455001	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4896832	0.95[JPT][hapmap]
rs4896837	0.95[JPT][hapmap]
rs4896838	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6570692	0.81[ASN][1000 genomes]
rs6570701	0.95[JPT][hapmap]
rs6570708	0.95[JPT][hapmap]
rs6900040	0.81[ASN][1000 genomes]
rs6901888	0.95[JPT][hapmap]
rs6902410	0.81[ASN][1000 genomes]
rs6906258	0.95[JPT][hapmap]
rs6906402	0.95[JPT][hapmap]
rs6912079	0.81[ASN][1000 genomes]
rs6913727	0.81[ASN][1000 genomes]
rs6915094	0.81[ASN][1000 genomes]
rs6923074	0.81[ASN][1000 genomes]
rs6925594	0.81[ASN][1000 genomes]
rs6930154	0.95[JPT][hapmap]
rs6941429	0.95[JPT][hapmap]
rs697053	0.95[JPT][hapmap]
rs697054	0.95[JPT][hapmap]
rs697055	0.95[JPT][hapmap]
rs702304	0.95[JPT][hapmap]
rs702306	0.94[JPT][hapmap]
rs702307	0.95[JPT][hapmap]
rs702316	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs702318	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs702319	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs702322	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs702324	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs719030	0.81[AMR][1000 genomes]
rs7746330	0.81[ASN][1000 genomes]
rs7752286	0.95[JPT][hapmap]
rs7753273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7753770	0.95[JPT][hapmap]
rs857875	0.95[JPT][hapmap]
rs857877	0.95[JPT][hapmap]
rs857880	0.95[JPT][hapmap]
rs857881	0.95[JPT][hapmap]
rs857882	0.95[JPT][hapmap]
rs857883	0.95[JPT][hapmap]
rs867056	0.89[EUR][1000 genomes]
rs9322029	0.81[ASN][1000 genomes]
rs9373463	0.81[ASN][1000 genomes]
rs9373467	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9376950	0.81[ASN][1000 genomes]
rs9376951	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376961	0.95[JPT][hapmap]
rs9390343	0.81[JPT][hapmap]
rs9399553	0.81[ASN][1000 genomes]
rs9399561	0.95[JPT][hapmap]
rs9403730	0.81[ASN][1000 genomes]
rs9403737	0.95[JPT][hapmap]
rs9403739	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9403742	0.85[JPT][hapmap]
rs9485017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs9497315	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9497395	0.81[JPT][hapmap]
rs9497403	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];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	nsv886746	chr6:145815949-145920894	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv886747	chr6:145815949-145922777	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1028290	chr6:145819982-145911857	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv886748	chr6:145835917-145911730	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9403725	SHPRH	cis	cerebellum	SCAN
rs9403725	EPM2A	cis	parietal	SCAN
rs9403725	SHPRH	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145890600-145904600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:145897400-145898000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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