Variant report

Variant	rs12666317
Chromosome Location	chr7:102704135-102704136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:102704001..102706200-chr7:102714762..102716967,2	K562	blood:
2	chr7:102691392..102694110-chr7:102703544..102706469,2	K562	blood:
3	chr7:102701175..102706120-chr7:102711307..102716730,7	K562	blood:
4	chr7:102611593..102615684-chr7:102700169..102704441,4	K562	blood:
5	chr7:102702765..102704335-chr7:102714764..102716771,2	MCF-7	breast:
6	chr7:102676967..102679361-chr7:102702578..102705004,2	K562	blood:
7	chr7:102389656..102391894-chr7:102702213..102705034,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222011	Chromatin interaction
ENSG00000161040	Chromatin interaction
ENSG00000230257	Chromatin interaction
ENSG00000170632	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10241865	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs10242028	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10273725	0.81[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs10808120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953380	0.84[ASN][1000 genomes]
rs10953382	0.83[ASN][1000 genomes]
rs11514917	0.87[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs11768949	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11770319	0.86[ASN][1000 genomes]
rs11972261	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs11976237	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs12537977	0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs13221585	0.97[ASN][1000 genomes]
rs13221979	0.84[ASN][1000 genomes]
rs13222980	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229214	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13232194	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13233521	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs13242493	0.93[CHD][hapmap];0.91[JPT][hapmap]
rs1608651	0.86[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs1829957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2222539	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298854	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41501847	0.81[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap]
rs4609128	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4620204	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs4729860	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4729866	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4729873	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs6465878	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6465885	0.82[GIH][hapmap]
rs6947403	0.81[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs6953980	0.81[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap]
rs6960428	0.80[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs6978630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7458786	0.93[ASN][1000 genomes]
rs7780405	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7785272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs7789252	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7794668	0.90[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap]
rs7796678	0.81[ASN][1000 genomes]
rs7807055	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs847646	0.91[JPT][hapmap]
rs847647	0.81[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs847648	0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs847649	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs847656	0.81[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs847658	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs869332	0.86[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs952879	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs955992	0.84[ASN][1000 genomes]
rs9718453	0.87[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv1793320	chr7:102677917-102706209	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv526764	chr7:102701826-102737251	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12666317	LRRC17	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102679200-102713800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:102684200-102708000	Weak transcription	Pancreas	Pancrea
3	chr7:102692800-102712800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr7:102702200-102713800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:102702200-102714600	Weak transcription	Ovary	ovary

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