Variant report

Variant	rs17177953
Chromosome Location	chr7:139491967-139491968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:139479210..139481182-chr7:139491846..139493959,3	K562	blood:
2	chr7:139486823..139488377-chr7:139490221..139491972,2	MCF-7	breast:
3	chr7:139485450..139487997-chr7:139490287..139492572,3	K562	blood:
4	chr7:139490458..139492000-chr7:139496695..139498330,2	K562	blood:
5	chr7:139490500..139493379-chr7:139496695..139499079,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1015121	0.83[AMR][1000 genomes]
rs10224408	0.90[GIH][hapmap];0.87[TSI][hapmap]
rs10278124	0.82[CEU][hapmap]
rs10487662	0.87[CEU][hapmap]
rs1106768	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12155449	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12374779	0.83[AMR][1000 genomes]
rs12374780	0.83[AMR][1000 genomes]
rs17177103	0.93[AMR][1000 genomes]
rs17177358	0.83[AMR][1000 genomes]
rs17178226	0.87[CEU][hapmap]
rs17178522	0.87[CEU][hapmap]
rs17178543	0.87[CEU][hapmap]
rs17262390	0.83[AMR][1000 genomes]
rs17262662	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17262676	0.81[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4074826	0.82[CEU][hapmap]
rs4074827	0.82[CEU][hapmap]
rs55826011	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56079671	0.86[AMR][1000 genomes]
rs61054086	0.83[AMR][1000 genomes]
rs6953224	0.87[CEU][hapmap]
rs6967634	0.93[AMR][1000 genomes]
rs73735624	0.83[EUR][1000 genomes]
rs740818	0.93[AMR][1000 genomes]
rs7793114	0.93[AMR][1000 genomes]
rs7798740	0.83[AMR][1000 genomes]
rs9769817	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv464732	chr7:139424022-139654256	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv608472	chr7:139424022-139654256	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018712	chr7:139429703-139658014	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv464733	chr7:139491967-139539218	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv608473	chr7:139491967-139539218	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17177953	LOC730441	cis	parietal	SCAN
rs17177953	RAB19	cis	parietal	SCAN
rs17177953	TBXAS1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139479000-139497400	Weak transcription	NH-A	brain
2	chr7:139483400-139497600	Weak transcription	Fetal Kidney	kidney
3	chr7:139483600-139492000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr7:139484800-139499000	Weak transcription	A549	lung
5	chr7:139485000-139497800	Weak transcription	NHEK	skin
6	chr7:139485000-139498000	Weak transcription	HMEC	breast
7	chr7:139485000-139502200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:139485600-139495400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:139485800-139499600	Weak transcription	Aorta	Aorta
10	chr7:139487200-139493600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:139488600-139498000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:139488800-139498400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:139489400-139498000	Weak transcription	Esophagus	oesophagus
14	chr7:139489400-139502600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:139491200-139492000	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr7:139491200-139492600	Enhancers	Skeletal Muscle Female	skeletal muscle

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