Variant report

Variant	rs1992207
Chromosome Location	chr12:104243345-104243346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104242967..104244745-chr12:104247327..104248982,2	K562	blood:
2	chr12:104234058..104237710-chr12:104241927..104245166,3	MCF-7	breast:
3	chr12:104232946..104237794-chr12:104239535..104249085,16	K562	blood:
4	chr12:104242898..104244862-chr12:104245301..104247034,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1165593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12812668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12816512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12816861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12822228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12822539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1370411	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1370413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1370775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17034734	0.97[ASN][1000 genomes]
rs1992208	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2118312	0.88[ASN][1000 genomes]
rs2252325	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2252327	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2255296	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255303	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2255315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255316	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2256160	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2256303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2438111	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2438112	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2438113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2438114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2438388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2578010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35015549	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4453308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4453309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4964302	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4964304	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71466281	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71466282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71466283	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7973043	0.92[ASN][1000 genomes]
rs7973278	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7973401	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1992207	MIR3652	cis	Esophagus Mucosa	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104236000-104245000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:104236000-104252600	Weak transcription	Esophagus	oesophagus
3	chr12:104236000-104252600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:104236000-104253600	Weak transcription	Gastric	stomach
5	chr12:104236200-104246400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:104236400-104245000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:104236400-104246000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:104236600-104248400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:104238200-104246400	Weak transcription	Fetal Intestine Large	intestine
10	chr12:104240000-104243400	Enhancers	Colon Smooth Muscle	Colon
11	chr12:104240000-104247600	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr12:104240000-104254800	Enhancers	Rectal Smooth Muscle	rectum
13	chr12:104240800-104245800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:104241200-104243600	Enhancers	HepG2	liver
15	chr12:104241800-104246400	Weak transcription	Fetal Intestine Small	intestine
16	chr12:104242200-104246400	Weak transcription	Fetal Lung	lung
17	chr12:104242200-104248400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:104242400-104244400	Weak transcription	Brain Anterior Caudate	brain
19	chr12:104242400-104244600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:104242400-104244600	Enhancers	Stomach Smooth Muscle	stomach
21	chr12:104242400-104245000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:104242400-104246400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:104242600-104243800	Enhancers	Fetal Stomach	stomach
24	chr12:104242600-104244600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr12:104242600-104246800	Enhancers	HMEC	breast
26	chr12:104242800-104243600	Enhancers	Aorta	Aorta
27	chr12:104242800-104244600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:104242800-104246200	Weak transcription	Pancreas	Pancrea
29	chr12:104242800-104247000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr12:104243000-104243400	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr12:104243000-104243400	Enhancers	HSMMtube	muscle
32	chr12:104243000-104244400	Weak transcription	Liver	Liver
33	chr12:104243000-104246000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:104243200-104243400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr12:104243200-104243600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:104243200-104244600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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