Variant report

Variant	rs4148856
Chromosome Location	chr12:123450765-123450766
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123428831..123431560-chr12:123448558..123451555,2	K562	blood:
2	chr12:123318760..123321217-chr12:123449684..123452450,2	K562	blood:
3	chr12:123449701..123452611-chr12:123716445..123719411,3	K562	blood:
4	chr12:123443368..123448710-chr12:123448756..123452152,6	MCF-7	breast:
5	chr12:123319262..123321924-chr12:123450152..123453465,3	K562	blood:
6	chr12:123355640..123358495-chr12:123449218..123452212,2	MCF-7	breast:
7	chr12:123428831..123432471-chr12:123448558..123452277,3	K562	blood:
8	chr12:123450564..123451345-chr15:90727982..90728518,2	Hela-S3	cervix:
9	chr12:123449477..123453379-chr12:123715163..123718004,4	MCF-7	breast:
10	chr12:123449665..123451282-chr12:123753748..123757462,3	MCF-7	breast:
11	chr12:123449332..123452871-chr12:123717386..123719515,4	K562	blood:
12	chr12:122983924..122985565-chr12:123450706..123452240,2	MCF-7	breast:
13	chr12:123373192..123374846-chr12:123449556..123451152,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150967	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000185033	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000139722	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12811109	0.92[EUR][1000 genomes]
rs12820906	0.92[ASN][1000 genomes]
rs12828755	0.91[EUR][1000 genomes]
rs1463877	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2270789	0.83[ASN][1000 genomes]
rs520088	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs655293	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71444568	0.85[EUR][1000 genomes]
rs883263	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs883563	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs937564	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs940904	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4148856	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs4148856	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs4148856	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs4148856	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs4148856	MPHOSPH9	cis	Esophagus Muscularis	GTEx
rs4148856	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs4148856	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs4148856	SBNO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123445800-123450800	Enhancers	Stomach Mucosa	stomach
2	chr12:123446000-123451400	Enhancers	Fetal Heart	heart
3	chr12:123448800-123450800	Flanking Active TSS	Brain Hippocampus Middle	brain
4	chr12:123449400-123450800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:123449600-123450800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:123449600-123450800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:123449800-123450800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr12:123449800-123450800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:123449800-123450800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:123449800-123451000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:123449800-123451000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr12:123449800-123451000	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr12:123449800-123451000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr12:123449800-123451000	Flanking Active TSS	Dnd41	blood
15	chr12:123449800-123451400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:123449800-123451400	Active TSS	Osteobl	bone
17	chr12:123450000-123450800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:123450000-123450800	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr12:123450000-123451000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:123450000-123451000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:123450000-123451000	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr12:123450000-123451000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr12:123450000-123451000	Flanking Active TSS	Colonic Mucosa	Colon
24	chr12:123450000-123451000	Active TSS	Colon Smooth Muscle	Colon
25	chr12:123450000-123451000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr12:123450000-123451000	Flanking Active TSS	Fetal Intestine Small	intestine
27	chr12:123450000-123451000	Flanking Active TSS	Fetal Muscle Leg	muscle
28	chr12:123450000-123451000	Flanking Active TSS	Fetal Stomach	stomach
29	chr12:123450000-123451000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr12:123450000-123451000	Flanking Active TSS	NH-A	brain
31	chr12:123450000-123451000	Active TSS	NHDF-Ad	bronchial
32	chr12:123450000-123451200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr12:123450000-123451400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:123450000-123451400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:123450000-123451400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:123450200-123450800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr12:123450200-123450800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr12:123450200-123450800	Flanking Active TSS	HUVEC	blood vessel
39	chr12:123450200-123451000	Active TSS	H9 Cell Line	embryonic stem cell
40	chr12:123450200-123451000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr12:123450200-123451000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr12:123450200-123451000	Flanking Active TSS	Fetal Thymus	thymus
43	chr12:123450200-123451000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
44	chr12:123450200-123451000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr12:123450200-123451000	Flanking Active TSS	Right Ventricle	heart
46	chr12:123450200-123451000	Active TSS	NHLF	lung
47	chr12:123450200-123451200	Active TSS	Fetal Brain Female	brain
48	chr12:123450200-123451200	Active TSS	HepG2	liver
49	chr12:123450200-123451400	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr12:123450200-123451400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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