Variant report

Variant	rs1148425
Chromosome Location	chr12:106643941-106643942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:106641572-106644424	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:106640579-106644067	GM19193	blood:	n/a	n/a
3	POLR2A	chr12:106641025-106644169	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:106640869-106644014	GM18951	blood:	n/a	n/a
5	POLR2A	chr12:106640930-106644009	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:106640929-106644016	GM15510	blood:	n/a	n/a
7	POLR2A	chr12:106640974-106643979	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:106634944..106646449-chr12:106667585..106679535,27	MCF-7	breast:
2	chr12:106640063..106644049-chr12:106694395..106698756,11	MCF-7	breast:
3	chr12:106639346..106644112-chr12:106694122..106698214,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258355	TF binding region
CKAP4	TF binding region
ENSG00000238609	Chromatin interaction
ENSG00000166046	Chromatin interaction
ENSG00000136026	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1148416	0.83[EUR][1000 genomes]
rs1148420	1.00[ASN][1000 genomes]
rs1148424	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1215754	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1215755	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1230058	1.00[ASN][1000 genomes]
rs12711453	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823591	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704897	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704899	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912748	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912749	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936702	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952114	1.00[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	esv1799917	chr12:106637876-106649988	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1834434	chr12:106637876-106649988	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106642000-106644000	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr12:106642200-106644200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr12:106642400-106644200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr12:106642600-106644000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:106642600-106644400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr12:106642800-106644000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:106642800-106644000	Enhancers	Left Ventricle	heart
8	chr12:106642800-106644000	Enhancers	Stomach Mucosa	stomach
9	chr12:106642800-106645400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:106642800-106647600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:106642800-106647800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:106642800-106648400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:106643000-106644000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:106643000-106644200	Enhancers	Fetal Heart	heart
15	chr12:106643000-106644400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr12:106643000-106644400	Enhancers	Fetal Muscle Leg	muscle
17	chr12:106643000-106645200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:106643000-106646400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:106643000-106647800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:106643200-106644000	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:106643200-106644000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr12:106643200-106644200	Weak transcription	Colonic Mucosa	Colon
23	chr12:106643200-106644200	Enhancers	Duodenum Mucosa	Duodenum
24	chr12:106643200-106644400	Weak transcription	Fetal Brain Female	brain
25	chr12:106643200-106644800	Weak transcription	HSMMtube	muscle
26	chr12:106643200-106645000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:106643200-106645000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:106643200-106645200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:106643200-106645200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:106643200-106645400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:106643200-106645400	Weak transcription	Brain Substantia Nigra	brain
32	chr12:106643200-106645400	Weak transcription	HSMM	muscle
33	chr12:106643200-106645600	Weak transcription	NHLF	lung
34	chr12:106643200-106645800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:106643200-106645800	Enhancers	Primary B cells from peripheral blood	blood
36	chr12:106643200-106646600	Weak transcription	NHEK	skin
37	chr12:106643200-106647200	Weak transcription	Aorta	Aorta
38	chr12:106643200-106647800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:106643200-106647800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:106643200-106647800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:106643200-106648800	Weak transcription	Right Atrium	heart
42	chr12:106643400-106644200	Enhancers	Ovary	ovary
43	chr12:106643400-106644200	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr12:106643400-106644600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:106643400-106644800	Weak transcription	NHDF-Ad	bronchial
46	chr12:106643400-106645000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:106643400-106645000	Weak transcription	Fetal Kidney	kidney
48	chr12:106643400-106645000	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr12:106643400-106645000	Weak transcription	Osteobl	bone
50	chr12:106643400-106645200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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