Variant report

Variant	rs12298976
Chromosome Location	chr12:120643705-120643706
allele	A/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	chr12:120643652-120645900	U87	brain:	n/a	n/a
2	POLR2A	chr12:120643637-120645894	U87	brain:	n/a	n/a
3	POLR2A	chr12:120643460-120646020	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr12:120643386-120645949	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120642171..120684465-chr12:120719749..120734210,267	K562	blood:
2	chr12:120642676..120646805-chr12:120725565..120732317,8	K562	blood:
3	chr12:120643126..120645367-chr12:120729894..120731522,2	MCF-7	breast:

Variant related genes	Relation type
RPLP0	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10128770	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs11065033	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11065038	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11065052	0.93[AFR][1000 genomes]
rs1151826	0.81[AFR][1000 genomes]
rs1151828	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1151831	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12297328	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12319440	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs1634820	1.00[YRI][hapmap]
rs2524389	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7957942	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active 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	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS 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	484 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120639600-120651400	Weak transcription	Stomach Mucosa	stomach
2	chr12:120639800-120644000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:120639800-120644000	Weak transcription	Ovary	ovary
4	chr12:120639800-120644800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:120639800-120645000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:120639800-120645000	Weak transcription	Lung	lung
7	chr12:120639800-120647600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:120639800-120647600	Weak transcription	Esophagus	oesophagus
9	chr12:120639800-120647600	Weak transcription	Gastric	stomach
10	chr12:120639800-120647600	Weak transcription	Left Ventricle	heart
11	chr12:120639800-120647600	Weak transcription	Right Ventricle	heart
12	chr12:120639800-120647600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:120639800-120647600	Weak transcription	Spleen	Spleen
14	chr12:120639800-120647600	Weak transcription	HSMMtube	muscle
15	chr12:120639800-120647800	Weak transcription	Aorta	Aorta
16	chr12:120639800-120648000	Weak transcription	Psoas Muscle	Psoas
17	chr12:120639800-120648400	Weak transcription	Small Intestine	intestine
18	chr12:120640000-120644800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:120640000-120647600	Weak transcription	Colonic Mucosa	Colon
20	chr12:120640000-120647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:120640000-120647800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:120640000-120648000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:120640000-120650000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:120640000-120650200	Weak transcription	Brain Substantia Nigra	brain
25	chr12:120640200-120643800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:120640200-120643800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:120640200-120643800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:120640200-120643800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:120640200-120643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:120640200-120643800	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:120640200-120643800	Weak transcription	HSMM	muscle
32	chr12:120640200-120644000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:120640200-120644000	Weak transcription	Fetal Intestine Small	intestine
34	chr12:120640200-120644000	Weak transcription	Fetal Lung	lung
35	chr12:120640200-120644000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:120640200-120644200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:120640200-120644200	Weak transcription	Adipose Nuclei	Adipose
38	chr12:120640200-120644200	Weak transcription	Brain Anterior Caudate	brain
39	chr12:120640200-120644200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:120640200-120644200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:120640200-120644200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr12:120640200-120644200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:120640200-120644200	Weak transcription	Fetal Brain Female	brain
44	chr12:120640200-120644200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:120640200-120644400	Weak transcription	Osteobl	bone
46	chr12:120640200-120644800	Weak transcription	Fetal Intestine Large	intestine
47	chr12:120640200-120644800	Weak transcription	Thymus	Thymus
48	chr12:120640200-120645200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr12:120640200-120645200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:120640200-120645200	Weak transcription	Rectal Mucosa Donor 29	rectum

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