Variant report

Variant	rs12298261
Chromosome Location	chr12:10129002-10129003
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1060648	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1075996	0.81[TSI][hapmap]
rs1359081	1.00[ASN][1000 genomes]
rs1807355	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs2401640	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2961544	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs3903806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903807	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611291	1.00[ASN][1000 genomes]
rs4764177	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4764187	0.89[GIH][hapmap]
rs476844	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs479499	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs531425	1.00[GIH][hapmap];0.82[TSI][hapmap]
rs545677	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570931	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574097	0.85[ASN][1000 genomes]
rs576031	0.81[ASN][1000 genomes]
rs588272	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs607567	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632963	0.82[ASN][1000 genomes]
rs633874	0.85[ASN][1000 genomes]
rs684134	0.85[ASN][1000 genomes]
rs7960084	0.89[GIH][hapmap]

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	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1038226	chr12:10121288-10143591	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1043125	chr12:10121288-10177037	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1042106	chr12:10121288-10177636	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1040610	chr12:10121288-10179374	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv525593	chr12:10121347-10156646	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12298261	GRIN2B	cis	parietal	SCAN
rs12298261	GABARAPL1	cis	cerebellum	SCAN
rs12298261	CLEC12A	cis	multi-tissue	Pritchard
rs12298261	PRB3	cis	cerebellum	SCAN
rs12298261	CLEC2D	cis	lymphoblastoid	seeQTL
rs12298261	ATN1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10127000-10129200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
2	chr12:10128000-10132600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
3	chr12:10128400-10129200	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
4	chr12:10128400-10129200	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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