Variant report

Variant	rs12867640
Chromosome Location	chr13:49216336-49216337
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1009719	0.92[ASN][1000 genomes]
rs12050047	0.92[ASN][1000 genomes]
rs12583212	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583622	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12585234	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12864882	0.94[ASN][1000 genomes]
rs12865846	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12867110	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12870838	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12870872	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12871411	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12871822	0.90[ASN][1000 genomes]
rs12876715	0.90[ASN][1000 genomes]
rs1326697	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1359107	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1476406	0.87[ASN][1000 genomes]
rs1980838	0.92[ASN][1000 genomes]
rs1980839	0.92[ASN][1000 genomes]
rs2146861	0.92[ASN][1000 genomes]
rs2148516	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34119347	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36088391	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59136233	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59927903	0.90[ASN][1000 genomes]
rs7331325	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334400	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7982278	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7987608	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7988330	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7989251	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535055	0.92[ASN][1000 genomes]
rs9535056	0.92[ASN][1000 genomes]
rs9535058	0.94[ASN][1000 genomes]
rs9535061	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9562835	0.87[ASN][1000 genomes]
rs9562836	0.87[ASN][1000 genomes]
rs9562837	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9562838	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9568057	0.92[ASN][1000 genomes]
rs9568060	0.92[ASN][1000 genomes]
rs9568063	0.92[ASN][1000 genomes]
rs9568066	0.90[ASN][1000 genomes]
rs9568067	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568068	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568070	0.90[ASN][1000 genomes]
rs9568071	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568072	0.90[ASN][1000 genomes]
rs9568075	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568077	0.87[ASN][1000 genomes]
rs9568079	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9634815	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634816	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634817	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9742182	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3495983	chr13:49181790-49222165	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3495984	chr13:49181790-49222165	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv525996	chr13:49210802-49222178	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12867640	CYSLTR2	cis	lymphoblastoid	seeQTL
rs12867640	C13orf18	cis	parietal	SCAN
rs12867640	LRCH1	cis	parietal	SCAN
rs12867640	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs12867640	ITM2B	cis	lymphoblastoid	seeQTL
rs12867640	C13orf1	cis	cerebellum	SCAN
rs12867640	LPAR6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49210800-49218000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:49214400-49217000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:49214800-49216400	Enhancers	K562	blood
4	chr13:49215200-49221000	Weak transcription	Dnd41	blood

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