Variant report

Variant	rs12623452
Chromosome Location	chr2:145435981-145435982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:145425002..145426621-chr2:145434784..145436814,2	K562	blood:
2	chr2:145268963..145271644-chr2:145434997..145436686,2	K562	blood:
3	chr2:145415897..145417567-chr2:145434431..145436385,2	K562	blood:

Variant related genes	Relation type
ENSG00000226674	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10200647	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10203655	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10205995	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10432351	0.82[ASN][1000 genomes]
rs10496966	0.92[ASN][1000 genomes]
rs10928225	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10928226	0.94[ASN][1000 genomes]
rs10928227	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs11674690	0.81[ASN][1000 genomes]
rs11679253	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11883829	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap]
rs11900456	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11902294	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12104619	0.89[ASN][1000 genomes]
rs12471698	0.93[ASN][1000 genomes]
rs12478142	0.93[ASN][1000 genomes]
rs12611966	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12991932	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12997597	0.97[ASN][1000 genomes]
rs13003467	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13008442	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13015001	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs13016064	0.92[ASN][1000 genomes]
rs13032840	0.91[ASN][1000 genomes]
rs13413613	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1351734	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1365902	0.90[ASN][1000 genomes]
rs1365905	0.92[ASN][1000 genomes]
rs1384779	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1384783	0.93[ASN][1000 genomes]
rs1427509	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs1483491	0.92[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs1483499	0.83[ASN][1000 genomes]
rs1529386	0.95[ASN][1000 genomes]
rs1529387	0.95[ASN][1000 genomes]
rs1559961	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559962	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564697	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs1896453	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1896454	0.95[ASN][1000 genomes]
rs1905347	0.82[ASN][1000 genomes]
rs1994155	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2086748	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2195114	0.92[ASN][1000 genomes]
rs2195115	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254435	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2381651	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs35099259	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856364	0.90[ASN][1000 genomes]
rs4458150	0.85[ASN][1000 genomes]
rs4471836	0.93[ASN][1000 genomes]
rs4662231	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4662232	0.92[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs4662393	0.88[ASN][1000 genomes]
rs61440197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6707047	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6728198	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6745079	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72991962	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7575857	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7579453	0.92[ASN][1000 genomes]
rs7580571	0.93[ASN][1000 genomes]
rs900554	1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs958500	0.93[ASN][1000 genomes]
rs958501	0.93[ASN][1000 genomes]
rs980772	1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs990847	1.00[CHB][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948474	chr2:145035890-145436665	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1002563	chr2:145182201-145863253	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv535957	chr2:145182201-145863253	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv529501	chr2:145257682-145485605	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12623452	ACVR2A	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145423000-145440600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:145433000-145438800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr2:145434000-145438600	Weak transcription	HMEC	breast
4	chr2:145434000-145439000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:145434200-145438600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:145434200-145439600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:145434400-145438400	Weak transcription	NHEK	skin
8	chr2:145435000-145436800	Enhancers	Fetal Intestine Large	intestine
9	chr2:145435400-145436000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr2:145435400-145436000	Weak transcription	Fetal Intestine Small	intestine
11	chr2:145435400-145436200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:145435400-145436600	Enhancers	Fetal Kidney	kidney

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