Variant report

Variant	rs40927
Chromosome Location	chr7:108190995-108190996
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108166940..108169062-chr7:108189842..108192603,2	K562	blood:
2	chr7:108190740..108192459-chr7:108199194..108201083,2	MCF-7	breast:
3	chr7:108175205..108176864-chr7:108190945..108193646,2	K562	blood:
4	chr7:108184554..108188738-chr7:108190088..108193231,5	K562	blood:

Variant related genes	Relation type
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10156002	0.86[CEU][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10253210	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10270723	0.89[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10282368	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1043615	0.89[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17426315	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]
rs1859772	0.83[YRI][hapmap]
rs194586	0.82[YRI][hapmap]
rs2041003	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072212	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2396001	0.83[YRI][hapmap]
rs34668718	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40856	0.83[YRI][hapmap]
rs40903	0.94[YRI][hapmap]
rs40911	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40913	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40916	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40918	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs40922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40930	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40933	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40937	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40943	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730324	0.82[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.81[ASN][1000 genomes]
rs6466239	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs40927	THAP5	cis	cerebellum	SCAN
rs40927	THAP5	cis	lymphoblastoid	seeQTL
rs40927	C7orf66	cis	cerebellum	SCAN
rs40927	RINT1	cis	cerebellum	SCAN
rs40927	DNAJB9	cis	parietal	SCAN
rs40927	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs40927	THAP5	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108189000-108196800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr7:108190200-108195400	Weak transcription	Left Ventricle	heart
3	chr7:108190200-108201400	Weak transcription	HSMMtube	muscle

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