Variant report

Variant	rs17426315
Chromosome Location	chr7:108225047-108225048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108208678..108213209-chr7:108221892..108226681,7	MCF-7	breast:
2	chr7:108225047..108227577-chr7:108235329..108237034,2	K562	blood:
3	chr7:108221854..108223398-chr7:108224330..108226111,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128590	Chromatin interaction
ENSG00000177683	Chromatin interaction
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10156002	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253210	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10270723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10282368	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1043615	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860118	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[YRI][hapmap]
rs2041003	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072212	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34668718	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40911	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs40913	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs40916	0.92[CEU][hapmap];0.85[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs40918	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs40922	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40927	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40929	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40930	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40933	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40937	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40943	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730324	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.92[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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3333624	chr7:108224566-108226814	Weak transcription Enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17426315	THAP5	cis	lymphoblastoid	seeQTL
rs17426315	THAP5	cis	cerebellum	SCAN
rs17426315	THAP5	cis	multi-tissue	Pritchard
rs17426315	DNAJB9	cis	parietal	SCAN
rs17426315	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs17426315	C7orf66	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108216400-108229400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:108221000-108229000	Weak transcription	Right Ventricle	heart
3	chr7:108221200-108226200	Weak transcription	Right Atrium	heart
4	chr7:108221200-108229200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:108223000-108233200	Weak transcription	Small Intestine	intestine
6	chr7:108224600-108225200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:108224800-108225800	Weak transcription	NHEK	skin
8	chr7:108225000-108225200	Enhancers	Fetal Heart	heart
9	chr7:108225000-108230400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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