Variant report

Variant	rs12661782
Chromosome Location	chr6:28466442-28466443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28464198..28466442-chr6:28581711..28584607,3	K562	blood:

Variant related genes	Relation type
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10484541	1.00[YRI][hapmap]
rs12660763	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12663002	0.81[CHD][hapmap]
rs16894139	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs16894166	0.81[AMR][1000 genomes]
rs17315739	1.00[YRI][hapmap]
rs17393066	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs2064424	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071966	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2078035	0.83[EUR][1000 genomes]
rs2078439	0.86[EUR][1000 genomes]
rs2227228	0.83[CHD][hapmap]
rs2232419	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs2273106	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28382604	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2859355	0.83[CHD][hapmap]
rs2859356	0.85[CHD][hapmap]
rs35327256	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35403242	0.90[AFR][1000 genomes]
rs35604709	0.80[AFR][1000 genomes]
rs35921765	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs377514	0.83[EUR][1000 genomes]
rs4711174	0.81[AFR][1000 genomes]
rs4711175	0.85[AFR][1000 genomes]
rs4713166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62402370	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62402378	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62402381	0.81[AFR][1000 genomes]
rs6921021	0.86[EUR][1000 genomes]
rs6933732	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6942252	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs72844230	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs769189	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468385	1.00[CEU][hapmap];0.91[CHD][hapmap];0.88[EUR][1000 genomes]
rs974334	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12661782	BTN2A3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28465600-28466600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:28465600-28466600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:28466400-28473000	Weak transcription	K562	blood

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