Variant report

Variant	rs1029708
Chromosome Location	chr7:108252714-108252715
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:108209177..108212583-chr7:108250280..108255068,5	MCF-7	breast:
2	chr7:108210096..108212539-chr7:108250642..108252871,3	MCF-7	breast:

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

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1029707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11767037	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11767071	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773524	0.85[ASN][1000 genomes]
rs11773875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17341955	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17426638	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108731	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2215141	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34505662	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298438	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55760662	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58954269	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466244	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67940245	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945788	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6949766	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951751	0.83[ASN][1000 genomes]
rs726608	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790890	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975124	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9768342	0.82[ASN][1000 genomes]
rs9918599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv1792680	chr7:108246985-108254739	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv275371	chr7:108250854-108257413	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1029708	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108249200-108254800	Enhancers	Liver	Liver
2	chr7:108251000-108252800	Enhancers	Placenta	Placenta
3	chr7:108251400-108254000	Enhancers	Brain Germinal Matrix	brain
4	chr7:108252000-108254200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:108252000-108255000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:108252200-108255000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:108252600-108253800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:108252600-108254200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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