Variant report

Variant	rs2438114
Chromosome Location	chr12:104246441-104246442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104233313..104235106-chr12:104245857..104249514,3	MCF-7	breast:
2	chr12:104232946..104237794-chr12:104239535..104249085,16	K562	blood:
3	chr12:104244166..104246985-chr12:104247469..104250168,2	MCF-7	breast:
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];0.94[ASN][1000 genomes]
rs12812668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12816512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12816861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12822228	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12822539	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1370411	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1370413	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370775	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17034734	1.00[YRI][hapmap];0.99[ASN][1000 genomes]
rs1992207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992208	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2118312	0.90[ASN][1000 genomes]
rs2252325	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252327	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255296	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255303	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2255315	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255316	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255324	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255568	0.85[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255584	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255791	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255794	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255795	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255797	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255799	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255807	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256160	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2256303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2438111	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2438112	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2438113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2438388	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2578010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35015549	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4453308	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4453309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964302	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964304	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71466281	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71466282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71466283	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7973043	0.94[ASN][1000 genomes]
rs7973278	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7973401	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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
rs2438114	MIR3652	cis	Esophagus Mucosa	GTEx

Chromatin state (count:47 , 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	chr12:104236600-104248400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:104240000-104247600	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr12:104240000-104254800	Enhancers	Rectal Smooth Muscle	rectum
7	chr12:104242200-104248400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:104242600-104246800	Enhancers	HMEC	breast
9	chr12:104242800-104247000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr12:104243800-104251400	Enhancers	Colon Smooth Muscle	Colon
11	chr12:104244400-104246800	Enhancers	Brain Anterior Caudate	brain
12	chr12:104244400-104246800	Enhancers	Osteobl	bone
13	chr12:104244600-104247000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:104244800-104246600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:104244800-104246800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:104245000-104246800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:104245000-104246800	Enhancers	Brain Cingulate Gyrus	brain
18	chr12:104245000-104247000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr12:104245000-104250800	Enhancers	HepG2	liver
20	chr12:104245200-104247000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:104245200-104247000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:104245200-104252000	Enhancers	Stomach Smooth Muscle	stomach
23	chr12:104245600-104246800	Enhancers	Fetal Stomach	stomach
24	chr12:104245600-104246800	Enhancers	HSMM	muscle
25	chr12:104245600-104249400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:104245800-104246600	Enhancers	Brain Angular Gyrus	brain
27	chr12:104245800-104248200	Weak transcription	Liver	Liver
28	chr12:104246000-104246600	Enhancers	Brain Hippocampus Middle	brain
29	chr12:104246000-104246600	Enhancers	NHEK	skin
30	chr12:104246000-104246800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:104246000-104246800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr12:104246000-104246800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:104246000-104246800	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr12:104246200-104246600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:104246200-104246600	Weak transcription	NH-A	brain
36	chr12:104246200-104246800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr12:104246200-104246800	Enhancers	Pancreas	Pancrea
38	chr12:104246200-104247200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:104246400-104246600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:104246400-104246600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:104246400-104246600	Enhancers	Aorta	Aorta
42	chr12:104246400-104246600	Enhancers	Fetal Lung	lung
43	chr12:104246400-104246600	Enhancers	Lung	lung
44	chr12:104246400-104246800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:104246400-104246800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:104246400-104246800	Enhancers	Fetal Intestine Small	intestine
47	chr12:104246400-104252600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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