Variant report

Variant	rs17341955
Chromosome Location	chr7:108244962-108244963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108230124..108232941-chr7:108244344..108247256,2	K562	blood:
2	chr7:108243393..108246050-chr7:108248845..108250724,2	K562	blood:
3	chr7:108209290..108211017-chr7:108244692..108246466,2	K562	blood:
4	chr7:108234971..108237051-chr7:108243040..108246034,2	K562	blood:

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

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1029707	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1029708	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]
rs11767037	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11767071	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773524	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11773875	0.96[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]
rs17426638	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108731	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2215141	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34505662	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298438	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55760662	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58954269	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67940245	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945788	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6949766	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951751	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs726608	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727881	0.81[EUR][1000 genomes]
rs7790890	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795236	0.81[EUR][1000 genomes]
rs9690171	0.82[EUR][1000 genomes]
rs975124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9768342	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9918599	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17341955	THAP5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108240400-108245600	Weak transcription	Fetal Brain Male	brain
2	chr7:108243000-108245400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:108243600-108246200	Enhancers	Placenta	Placenta
4	chr7:108244000-108245000	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr7:108244000-108245800	Enhancers	Fetal Brain Female	brain
6	chr7:108244400-108246000	Enhancers	Brain Germinal Matrix	brain
7	chr7:108244400-108247800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:108244800-108245600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:108244800-108245600	Flanking Active TSS	K562	blood

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