Variant report

Variant	rs40929
Chromosome Location	chr7:108191704-108191705
allele	C/G
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	chr7:108191362..108206184-chr7:108206645..108216261,27	K562	blood:
5	chr7:108184554..108188738-chr7:108190088..108193231,5	K562	blood:

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

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10156002	0.87[CEU][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10253210	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10270723	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10282368	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1043615	0.88[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17426315	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2041003	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072212	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34668718	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40911	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40913	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40916	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40918	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs40922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40927	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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40933	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40937	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40943	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730324	0.81[CHB][hapmap];0.81[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs40929	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 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
4	chr7:108191000-108192400	Enhancers	Primary B cells from cord blood	blood
5	chr7:108191200-108192600	Enhancers	Primary B cells from peripheral blood	blood
6	chr7:108191400-108204600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:108191600-108196800	Weak transcription	Ovary	ovary

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