Variant report

Variant	rs7212447
Chromosome Location	chr17:17987067-17987068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17984958..17988016-chr17:17989575..17991247,3	MCF-7	breast:
2	chr17:17984941..17987120-chr17:17988485..17990982,3	MCF-7	breast:
3	chr17:17967495..17969681-chr17:17984631..17987078,2	K562	blood:

Variant related genes	Relation type
ENSG00000108591	Chromatin interaction
ENSG00000141034	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1008135	0.94[EUR][1000 genomes]
rs1101727	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078406	0.87[ASW][hapmap]
rs11078408	0.87[ASW][hapmap];0.85[CEU][hapmap]
rs11078410	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11650021	0.84[EUR][1000 genomes]
rs11867241	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11870660	0.85[CEU][hapmap]
rs12939020	0.82[EUR][1000 genomes]
rs2056842	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2955350	0.86[EUR][1000 genomes]
rs2955353	0.86[EUR][1000 genomes]
rs2955354	0.95[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs2955355	0.95[CEU][hapmap];0.91[GIH][hapmap];0.85[EUR][1000 genomes]
rs2955356	0.95[CEU][hapmap];0.91[GIH][hapmap];0.85[EUR][1000 genomes]
rs2955357	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2955358	0.95[CEU][hapmap];0.91[GIH][hapmap];0.85[EUR][1000 genomes]
rs2955359	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs2955365	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2955366	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2955367	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2955368	0.84[EUR][1000 genomes]
rs2955370	0.95[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs2955372	0.95[CEU][hapmap];0.91[GIH][hapmap];0.87[EUR][1000 genomes]
rs2955377	0.89[ASW][hapmap];0.90[CEU][hapmap];0.91[GIH][hapmap];0.81[EUR][1000 genomes]
rs2955378	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.81[EUR][1000 genomes]
rs2955380	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2955381	0.94[CEU][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs2955383	0.95[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes]
rs2955384	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes]
rs2955385	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes]
rs2974998	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2974999	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2975003	0.82[ASN][1000 genomes]
rs2975004	0.82[ASN][1000 genomes]
rs2975005	0.82[ASN][1000 genomes]
rs4072738	0.89[CEU][hapmap]
rs4072739	0.89[CEU][hapmap]
rs4299203	0.85[CEU][hapmap]
rs4365346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4368210	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap]
rs4410135	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4426402	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4459604	0.95[CEU][hapmap];0.91[GIH][hapmap]
rs4506967	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4506969	0.90[CEU][hapmap]
rs4561528	0.93[EUR][1000 genomes]
rs4584886	0.95[CEU][hapmap];0.91[GIH][hapmap]
rs4643387	0.87[EUR][1000 genomes]
rs4924832	0.95[CEU][hapmap];0.91[GIH][hapmap]
rs4925125	0.87[ASW][hapmap]
rs4925126	0.87[ASW][hapmap]
rs4925135	0.85[EUR][1000 genomes]
rs4925136	0.85[EUR][1000 genomes]
rs59518074	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62073573	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6502632	0.95[CEU][hapmap];0.91[GIH][hapmap]
rs6502633	0.84[EUR][1000 genomes]
rs6502634	0.82[EUR][1000 genomes]
rs6502636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6502637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6826	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712267	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712268	0.94[EUR][1000 genomes]
rs7207461	0.86[EUR][1000 genomes]
rs7207821	0.95[CEU][hapmap]
rs7209003	0.95[CEU][hapmap]
rs7210400	0.85[EUR][1000 genomes]
rs7211714	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7212167	0.95[CEU][hapmap];0.91[GIH][hapmap]
rs7215524	0.81[EUR][1000 genomes]
rs721669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7219320	0.81[GIH][hapmap]
rs7219324	0.89[CEU][hapmap]
rs7224047	0.83[EUR][1000 genomes]
rs7406744	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7406982	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs741782	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7503738	0.83[EUR][1000 genomes]
rs8066764	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8068175	0.85[CEU][hapmap]
rs8069811	0.81[EUR][1000 genomes]
rs8075189	0.95[CEU][hapmap]
rs8080602	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs854763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854767	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854768	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854769	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854770	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854789	0.94[EUR][1000 genomes]
rs854790	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854791	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs854792	0.83[EUR][1000 genomes]
rs854808	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854817	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854818	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9303144	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9894138	0.85[EUR][1000 genomes]
rs9896837	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.81[EUR][1000 genomes]
rs9897761	0.95[CEU][hapmap]
rs9899355	0.89[CEU][hapmap]
rs9913277	0.95[CEU][hapmap];0.91[GIH][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7212447	SREBF1	cis	Whole Blood	GTEx
rs7212447	TOM1L2	cis	parietal	SCAN
rs7212447	C17orf39	cis	cerebellum	SCAN
rs7212447	TOM1L2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17986400-17988400	Enhancers	Placenta	Placenta
2	chr17:17986800-17987400	Enhancers	HepG2	liver
3	chr17:17987000-17987200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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