Variant report

Variant	rs6760488
Chromosome Location	chr2:31434184-31434185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10186540	0.83[AMR][1000 genomes]
rs10186955	0.83[AMR][1000 genomes]
rs10188925	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10199433	0.83[AMR][1000 genomes]
rs10210276	0.83[AMR][1000 genomes]
rs11124254	0.83[AMR][1000 genomes]
rs11685796	0.81[AMR][1000 genomes]
rs11691586	0.83[AMR][1000 genomes]
rs11691591	0.83[AMR][1000 genomes]
rs13017123	0.81[AMR][1000 genomes]
rs1562022	1.00[JPT][hapmap]
rs17010826	1.00[JPT][hapmap]
rs2365214	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4951972	0.83[AMR][1000 genomes]
rs4951973	0.83[AMR][1000 genomes]
rs4951974	0.83[EUR][1000 genomes]
rs4952059	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4952062	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952063	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4952064	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4952065	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4952066	0.83[AMR][1000 genomes]
rs4952067	0.83[AMR][1000 genomes]
rs56238301	0.83[AMR][1000 genomes]
rs6711677	0.83[AMR][1000 genomes]
rs6726620	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6740128	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7559123	0.81[EUR][1000 genomes]
rs9789381	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv873775	chr2:31363732-31439443	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv873776	chr2:31384009-31439443	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv430635	chr2:31420415-31464385	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1009712	chr2:31424588-31468364	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1000416	chr2:31424588-31470845	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv581268	chr2:31425783-31467079	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1001299	chr2:31428030-31464385	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv430646	chr2:31428030-31464385	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6760488	GCKR	cis	cerebellum	SCAN
rs6760488	SNORD53	cis	cerebellum	SCAN
rs6760488	AGBL5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31411200-31436800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:31423400-31436800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:31424200-31435800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:31424200-31437600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:31428800-31437400	Weak transcription	Esophagus	oesophagus
6	chr2:31430200-31441600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:31431000-31436000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:31431000-31436000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:31431200-31436000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:31431600-31435800	Weak transcription	GM12878-XiMat	blood
11	chr2:31431800-31436800	Weak transcription	Primary B cells from cord blood	blood
12	chr2:31432000-31435800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:31432400-31436600	Weak transcription	Fetal Heart	heart
14	chr2:31432800-31435600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:31433800-31434400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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