Variant report

Variant	rs17733498
Chromosome Location	chr7:21064587-21064588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10265690	0.83[AFR][1000 genomes]
rs12113935	0.95[ASN][1000 genomes]
rs12700247	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13228761	0.95[ASN][1000 genomes]
rs13232210	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17675673	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17675913	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17676127	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17676175	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17732288	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17732809	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34346814	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34369077	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34388702	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34490482	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34562194	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34578613	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35289319	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35312925	0.95[ASN][1000 genomes]
rs35462998	0.95[ASN][1000 genomes]
rs35563344	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35831036	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36005121	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36070274	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3810893	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3827656	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4281024	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4598145	0.95[ASN][1000 genomes]
rs58620271	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6461528	0.95[ASN][1000 genomes]
rs6944551	0.95[ASN][1000 genomes]
rs71526346	0.83[EUR][1000 genomes]
rs71526347	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030726	chr7:20506095-21086719	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv830920	chr7:21014535-21201580	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv3478244	chr7:21044211-21417347	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3478245	chr7:21044211-21417347	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1020852	chr7:21060791-21375050	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv538799	chr7:21060791-21375050	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17733498	ITGB8	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21054400-21070000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:21060600-21067800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:21062800-21065200	Enhancers	Brain Germinal Matrix	brain
4	chr7:21063600-21064600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr7:21063600-21064800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr7:21063600-21065600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr7:21063600-21072400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:21063800-21064600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:21063800-21064800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr7:21063800-21065200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr7:21064000-21064600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:21064000-21064600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:21064000-21064800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr7:21064000-21065400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr7:21064000-21067000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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