Variant report

Variant	rs4964304
Chromosome Location	chr12:104252184-104252185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104234105..104239098-chr12:104250004..104255076,13	MCF-7	breast:
2	chr12:104247921..104249635-chr12:104251344..104253746,2	MCF-7	breast:
3	chr12:104250532..104253421-chr12:104255015..104257063,2	K562	blood:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1165593	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12812668	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12815289	0.83[ASN][1000 genomes]
rs12816512	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12816861	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12822228	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12822539	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1370411	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1370413	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1370775	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17034734	0.92[ASN][1000 genomes]
rs1992207	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992208	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2118312	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2252325	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2252327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255296	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255303	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2255315	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255316	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255324	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255568	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2255584	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255791	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255794	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255795	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255797	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255799	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255807	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2256160	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2256303	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2438111	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2438112	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2438113	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2438114	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2438388	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2578010	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35015549	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4453308	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4453309	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4964302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71466281	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71466282	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71466283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973043	0.98[ASN][1000 genomes]
rs7973278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4964304	C12orf73	cis	Artery Aorta	GTEx
rs4964304	MIR3652	cis	Esophagus Mucosa	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104236000-104252600	Weak transcription	Esophagus	oesophagus
2	chr12:104236000-104252600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:104236000-104253600	Weak transcription	Gastric	stomach
4	chr12:104240000-104254800	Enhancers	Rectal Smooth Muscle	rectum
5	chr12:104246400-104252600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:104246600-104252400	Weak transcription	NHEK	skin
7	chr12:104246600-104253200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:104246800-104252200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:104246800-104254000	Weak transcription	Brain Anterior Caudate	brain
10	chr12:104247800-104252200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:104248800-104252800	Weak transcription	Fetal Stomach	stomach
12	chr12:104249600-104252600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:104249800-104252200	Weak transcription	HMEC	breast
14	chr12:104249800-104252600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:104250000-104252600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:104250000-104257000	Weak transcription	Pancreas	Pancrea
17	chr12:104250000-104263800	Weak transcription	Liver	Liver
18	chr12:104250200-104252200	Weak transcription	HSMM	muscle
19	chr12:104250200-104252400	Weak transcription	NH-A	brain
20	chr12:104250400-104252400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:104250400-104254000	Weak transcription	Ovary	ovary
22	chr12:104250600-104252200	Weak transcription	Placenta	Placenta
23	chr12:104250600-104252600	Weak transcription	Osteobl	bone
24	chr12:104251000-104253400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:104251200-104254400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:104251400-104252800	Enhancers	HepG2	liver
27	chr12:104251400-104254400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:104251800-104252400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:104252000-104252200	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr12:104252000-104252400	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr12:104252000-104252600	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr12:104252000-104254000	Enhancers	HSMMtube	muscle
33	chr12:104252000-104254400	Enhancers	Muscle Satellite Cultured Cells	--

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