Variant report

Variant	rs3097412
Chromosome Location	chr4:74748288-74748289
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	chr4:74746733..74749613-chr4:74751019..74753569,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10007826	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021230	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10028419	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1366946	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366949	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850137	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2115691	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145615	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2367291	0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[YRI][hapmap]
rs2367293	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs24772	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2886927	0.81[ASW][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[YRI][hapmap]
rs2968710	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3097409	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3097411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs3111694	0.81[ASW][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[YRI][hapmap]
rs3111697	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111698	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3117597	0.90[JPT][hapmap];0.83[YRI][hapmap]
rs3117598	0.81[ASW][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[YRI][hapmap]
rs3117600	0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[YRI][hapmap]
rs3117604	0.83[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[YRI][hapmap]
rs4074	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs482239	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs492155	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs493091	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs508977	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs512606	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs516224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518632	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs519565	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs537373	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs541923	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs548068	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs551744	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs561454	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs562213	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs569390	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs573878	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs593641	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs596352	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs623659	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs634304	0.91[AMR][1000 genomes]
rs638767	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs654871	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs655328	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs673038	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs680044	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs680452	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs683671	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs684080	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6858086	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[ASN][1000 genomes]
rs7674809	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9991272	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv432612	chr4:74723372-74774372	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3097412	NPFFR2	cis	parietal	SCAN
rs3097412	SEPT11	cis	parietal	SCAN
rs3097412	ANKRD17	cis	cerebellum	SCAN
rs3097412	CXCL6	cis	parietal	SCAN
rs3097412	G3BP2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74736800-74749000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:74742000-74748600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:74746800-74748800	Weak transcription	NHEK	skin
4	chr4:74747000-74748800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:74747000-74749000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:74747600-74752200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:74747800-74749600	Enhancers	NHDF-Ad	bronchial
8	chr4:74748200-74749800	Enhancers	Dnd41	blood
9	chr4:74748200-74752000	Enhancers	Muscle Satellite Cultured Cells	--

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