Variant report

Variant	rs2267546
Chromosome Location	chr12:4745313-4745314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4743724..4745923-chr12:4752293..4755038,2	K562	blood:

Variant related genes	Relation type
ENSG00000256381	Chromatin interaction
ENSG00000111254	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10774250	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs10774255	0.89[TSI][hapmap]
rs11063260	0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs11063267	0.82[EUR][1000 genomes]
rs11063269	0.97[ASN][1000 genomes]
rs11608880	0.92[ASN][1000 genomes]
rs11612861	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs12424286	0.97[ASN][1000 genomes]
rs2072358	0.97[ASN][1000 genomes]
rs2109097	0.95[ASN][1000 genomes]
rs2159351	0.89[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs2159352	0.81[EUR][1000 genomes]
rs2267549	0.80[JPT][hapmap]
rs2270134	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2299835	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2302247	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs4147674	0.87[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4147681	0.81[EUR][1000 genomes]
rs4766261	0.84[CHB][hapmap];0.92[ASN][1000 genomes]
rs4766263	0.97[ASN][1000 genomes]
rs4766266	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55798490	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56118230	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66871237	0.97[ASN][1000 genomes]
rs67338449	0.92[ASN][1000 genomes]
rs714621	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs887307	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs979877	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv898617	chr12:4715082-4768619	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv468986	chr12:4726068-4751798	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv557124	chr12:4726068-4751798	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv898618	chr12:4726068-4764137	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv898619	chr12:4737715-4771456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv898620	chr12:4745313-4771456	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2267546	AKAP3	cis	cerebellum	SCAN
rs2267546	AKAP3	cis	parietal	SCAN
rs2267546	NDUFA9	cis	parietal	SCAN
rs2267546	ADIPOR2	cis	parietal	SCAN
rs2267546	AKAP3	Cis_1M	lymphoblastoid	RTeQTL
rs2267546	AKAP3	cis	lung	GTEx
rs2267546	AKAP3	cis	Skin Sun Exposed Lower leg	GTEx
rs2267546	NDUFA9	cis	cerebellum	SCAN
rs2267546	AKAP3	cis	lymphoblastoid	seeQTL
rs2267546	AKAP3	cis	Esophagus Mucosa	GTEx
rs2267546	AKAP3	cis	multi-tissue	Pritchard
rs2267546	AKAP3	cis	Esophagus Muscularis	GTEx
rs2267546	AKAP3	cis	Thyroid	GTEx
rs2267546	AKAP3	cis	Heart Left Ventricle	GTEx
rs2267546	AKAP3	cis	Stomach	GTEx
rs2267546	AKAP3	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4724200-4756800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr12:4725400-4752200	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:4737600-4757400	Weak transcription	Pancreas	Pancrea
4	chr12:4737800-4757200	Weak transcription	Brain Anterior Caudate	brain

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