Variant report

Variant	rs61938963
Chromosome Location	chr12:56446804-56446805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56435833..56437664-chr12:56444374..56447347,3	MCF-7	breast:
2	chr12:56439022..56443137-chr12:56446581..56450430,4	MCF-7	breast:
3	chr12:56446518..56448384-chr12:56473145..56475689,2	MCF-7	breast:
4	chr12:56446553..56448907-chr12:56510280..56512287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197728	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000229117	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10876866	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1131017	0.85[ASN][1000 genomes]
rs1689510	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1701704	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1702877	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2017445	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2292239	0.83[EUR][1000 genomes]
rs2456973	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2640562	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2640564	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34415530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741499	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4759229	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61938962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705696	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs705702	0.81[EUR][1000 genomes]
rs705704	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs705705	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7302200	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs772920	0.81[EUR][1000 genomes]
rs772921	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs877636	0.83[EUR][1000 genomes]

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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs61938963	AC034102.1	cis	Muscle Skeletal	GTEx
rs61938963	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs61938963	RAB5B	cis	Muscle Skeletal	GTEx
rs61938963	DEFB124	trans	lymphoblastoid	RTeQTL
rs61938963	SUOX	cis	Thyroid	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56437000-56447200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
3	chr12:56437800-56450000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:56439600-56447200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:56439600-56448800	Weak transcription	HSMMtube	muscle
6	chr12:56439600-56449600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:56439800-56448600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:56440000-56448600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:56440400-56448600	Weak transcription	HMEC	breast
10	chr12:56440600-56448400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:56440600-56448600	Weak transcription	A549	lung
12	chr12:56440800-56454000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:56440800-56455600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:56441000-56448400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:56441200-56448600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:56445400-56449600	Enhancers	Placenta	Placenta

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