Variant report

Variant	rs10491488
Chromosome Location	chr5:80252534-80252535
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10491490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12653956	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2015661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66484258	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6893705	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs888822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs888823	0.99[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10491488	RASGRF2	cis	cerebellum	SCAN
rs10491488	XRCC4	cis	cerebellum	SCAN
rs10491488	AP3B1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80248200-80252600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr5:80249000-80255000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:80251000-80252600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr5:80251000-80253800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr5:80251200-80252600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr5:80251200-80252600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr5:80251200-80252600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr5:80251200-80252800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:80251600-80255800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:80251800-80253400	Bivalent Enhancer	Brain Germinal Matrix	brain
11	chr5:80252000-80253000	Enhancers	NH-A	brain
12	chr5:80252000-80254000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:80252200-80253000	Enhancers	Brain Substantia Nigra	brain
14	chr5:80252200-80253400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:80252200-80254000	Enhancers	Primary T cells from cord blood	blood
16	chr5:80252400-80252600	Bivalent Enhancer	Fetal Kidney	kidney
17	chr5:80252400-80253000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr5:80252400-80253000	Bivalent Enhancer	HUVEC	blood vessel
19	chr5:80252400-80253400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:80252400-80253600	Enhancers	HepG2	liver
21	chr5:80252400-80254000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:80252400-80254000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr5:80252400-80255600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr5:80252400-80255600	Weak transcription	Ovary	ovary

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