Variant report

Variant	rs6509002
Chromosome Location	chr19:42358069-42358070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:42351673..42358248-chr19:42360570..42366998,12	K562	blood:
2	chr19:42354940..42358615-chr19:42368975..42372693,4	K562	blood:
3	chr19:42351659..42356119-chr19:42356243..42359283,5	K562	blood:
4	chr19:42356783..42358615-chr19:42370430..42372693,2	K562	blood:
5	chr19:42356986..42361396-chr19:42362042..42367037,5	MCF-7	breast:
6	chr19:42353854..42356119-chr19:42356862..42359201,2	K562	blood:
7	chr19:42347025..42349260-chr19:42357171..42359234,2	K562	blood:
8	chr19:42354648..42360278-chr19:42362159..42366781,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000183103	Chromatin interaction
ENSG00000142025	Chromatin interaction
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10404939	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10407206	0.81[ASN][1000 genomes]
rs10407797	0.80[ASN][1000 genomes]
rs10408367	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10414356	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10414823	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10416824	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10417985	0.90[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap]
rs10500284	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12976571	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12979253	0.87[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12984383	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs1366610	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap]
rs1457144	0.82[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1870092	0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs1870093	0.91[ASN][1000 genomes]
rs2008798	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2075750	0.91[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap]
rs2075752	0.90[ASW][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap]
rs2075754	0.91[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap]
rs2199829	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2290695	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305809	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28824227	0.85[ASN][1000 genomes]
rs3786536	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs3786538	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap]
rs3810153	0.87[CHB][hapmap]
rs3922888	0.82[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4130852	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803511	0.82[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803512	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58857981	0.81[ASN][1000 genomes]
rs6508999	0.85[ASN][1000 genomes]
rs6509000	0.85[ASN][1000 genomes]
rs6509001	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7248641	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7252877	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7254214	0.80[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs7257666	0.81[ASN][1000 genomes]
rs7259967	0.91[CHB][hapmap]
rs734107	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs8102670	0.80[ASN][1000 genomes]
rs8104958	0.82[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8106505	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs8113283	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs8113641	0.86[JPT][hapmap]
rs8113780	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs873282	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap]
rs882520	0.87[CHB][hapmap]
rs899662	0.81[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6509002	CA11	cis	cerebellum	SCAN
rs6509002	LIG1	cis	parietal	SCAN
rs6509002	ZNF575	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42352000-42363800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:42357800-42359400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:42358000-42358400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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