Variant report

Variant	rs17312515
Chromosome Location	chr20:40758042-40758043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:40753966..40756056-chr20:40757861..40760151,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12625736	0.89[ASW][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1569552	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs17221018	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs17221067	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17221137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17221326	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17221823	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs2092277	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2903466	0.85[CHD][hapmap]
rs4281967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56284628	0.80[ASN][1000 genomes]
rs59610476	0.94[ASN][1000 genomes]
rs6016698	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs6030012	0.80[ASN][1000 genomes]
rs6030014	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs6102693	0.82[CHB][hapmap];0.92[CHD][hapmap];0.80[ASN][1000 genomes]
rs6102696	0.80[ASN][1000 genomes]
rs6124418	0.86[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6130042	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs6130043	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs6130047	0.83[TSI][hapmap]
rs73114433	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73114444	0.94[ASN][1000 genomes]
rs73114449	0.94[ASN][1000 genomes]
rs73131127	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv3381	chr20:39925326-40765696	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats 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	34 gene(s)	inside rSNPs	diseases
2	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17312515	WFDC12	cis	cerebellum	SCAN
rs17312515	KCNS1	cis	parietal	SCAN
rs17312515	HNF4A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40747200-40758400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr20:40747800-40762400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr20:40757600-40765800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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