Variant report

Variant	rs17403547
Chromosome Location	chr2:186291818-186291819
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:186291344..186293651-chr2:186297486..186299914,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11675629	0.90[ASN][1000 genomes]
rs11676655	0.90[ASN][1000 genomes]
rs11681870	0.90[ASN][1000 genomes]
rs11686861	0.90[ASN][1000 genomes]
rs11691490	0.90[ASN][1000 genomes]
rs11691615	0.90[ASN][1000 genomes]
rs11693233	0.90[ASN][1000 genomes]
rs12988744	0.90[ASN][1000 genomes]
rs13014616	0.90[ASN][1000 genomes]
rs13014885	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13015110	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17331619	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17331682	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17403498	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403638	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34087779	0.90[ASN][1000 genomes]
rs34537855	0.90[ASN][1000 genomes]
rs34826735	0.90[ASN][1000 genomes]
rs34969380	0.90[ASN][1000 genomes]
rs35066265	0.90[ASN][1000 genomes]
rs35630311	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35815004	0.90[ASN][1000 genomes]
rs35871462	0.90[ASN][1000 genomes]
rs35920523	0.90[ASN][1000 genomes]
rs66759141	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs66941454	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6731674	0.90[ASN][1000 genomes]
rs67432566	0.90[ASN][1000 genomes]
rs67638453	0.90[ASN][1000 genomes]
rs67992386	0.90[ASN][1000 genomes]
rs71430186	0.90[ASN][1000 genomes]
rs72892419	0.90[ASN][1000 genomes]
rs72892423	0.90[ASN][1000 genomes]
rs72892438	0.90[ASN][1000 genomes]
rs72892443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584009	chr2:186203397-186345148	Active TSS Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv459982	chr2:186213755-186475590	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv584012	chr2:186213755-186475590	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875525	chr2:186223503-186434458	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv470502	chr2:186245653-186309738	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv459983	chr2:186245653-186377253	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv584013	chr2:186245653-186377253	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv524452	chr2:186258409-186297074	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv518379	chr2:186259653-186297074	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv875526	chr2:186272059-186434458	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv875527	chr2:186272059-186475590	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17403547	COL5A2	cis	cerebellum	SCAN
rs17403547	GULP1	cis	parietal	SCAN
rs17403547	PPP1R1C	cis	parietal	SCAN
rs17403547	ZC3H15	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186289600-186292000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr2:186289600-186292000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:186289600-186292000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:186289600-186292200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:186289800-186292400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:186290200-186292000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr2:186291000-186292200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:186291000-186295600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:186291200-186297800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:186291800-186292000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:186291800-186292000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
12	chr2:186291800-186292000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
13	chr2:186291800-186292000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:186291800-186292000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:186291800-186292000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr2:186291800-186292000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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