Variant report

Variant	rs12309480
Chromosome Location	chr12:56528529-56528530
allele	G/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	chr12:56528454-56528742	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56518356..56534331-chr12:56534720..56548698,49	MCF-7	breast:
2	chr12:56526190..56529140-chr12:56532502..56534555,3	MCF-7	breast:
3	chr12:56526232..56528705-chr12:56554027..56556054,3	MCF-7	breast:
4	chr12:56526078..56528976-chr12:56529698..56531999,2	MCF-7	breast:

Variant related genes	Relation type
ESYT1	TF binding region
ENSG00000092841	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000196465	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10129008	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10876878	1.00[EUR][1000 genomes]
rs11171746	0.85[AFR][1000 genomes]
rs11171754	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11171755	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11171777	1.00[EUR][1000 genomes]
rs11834728	1.00[EUR][1000 genomes]
rs12296387	0.82[AFR][1000 genomes]
rs12298136	0.85[AFR][1000 genomes]
rs12309692	0.85[AFR][1000 genomes]
rs12320265	1.00[EUR][1000 genomes]
rs1274502	1.00[EUR][1000 genomes]
rs1274503	1.00[EUR][1000 genomes]
rs1405859	1.00[EUR][1000 genomes]
rs2463365	1.00[EUR][1000 genomes]
rs2695783	1.00[EUR][1000 genomes]
rs28676339	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2930788	1.00[EUR][1000 genomes]
rs2950573	1.00[EUR][1000 genomes]
rs55887836	1.00[EUR][1000 genomes]
rs58009483	1.00[EUR][1000 genomes]
rs59420211	1.00[EUR][1000 genomes]
rs703823	1.00[EUR][1000 genomes]
rs73340401	1.00[EUR][1000 genomes]
rs74092003	1.00[EUR][1000 genomes]
rs7489249	1.00[EUR][1000 genomes]
rs773658	1.00[EUR][1000 genomes]
rs773659	1.00[EUR][1000 genomes]
rs773661	1.00[EUR][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56523200-56533400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56523600-56537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56523800-56537000	Weak transcription	Right Atrium	heart
4	chr12:56523800-56539400	Strong transcription	NHEK	skin
5	chr12:56524000-56528800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:56524000-56537000	Strong transcription	Fetal Intestine Small	intestine
7	chr12:56524200-56529200	Strong transcription	Brain Hippocampus Middle	brain
8	chr12:56524200-56539200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:56524200-56539200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:56524200-56539400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:56524200-56539400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:56524200-56539400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:56524200-56539400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:56524200-56539400	Strong transcription	NH-A	brain
15	chr12:56524400-56528800	Strong transcription	Osteobl	bone
16	chr12:56524400-56529000	Strong transcription	NHLF	lung
17	chr12:56524400-56535000	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr12:56524400-56535200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr12:56524400-56535200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:56524400-56535400	Strong transcription	Spleen	Spleen
21	chr12:56524400-56536600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr12:56524400-56536800	Strong transcription	HMEC	breast
23	chr12:56524400-56537000	Strong transcription	Fetal Intestine Large	intestine
24	chr12:56524400-56539000	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr12:56524400-56539000	Strong transcription	Rectal Smooth Muscle	rectum
26	chr12:56524400-56539000	Strong transcription	HSMMtube	muscle
27	chr12:56524400-56539200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:56524400-56539200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:56524400-56539200	Strong transcription	Fetal Stomach	stomach
30	chr12:56524400-56539400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:56524400-56539400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:56524400-56539400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:56524400-56539400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:56524400-56539400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:56524400-56539400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:56524400-56539400	Strong transcription	Liver	Liver
37	chr12:56524400-56539600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:56524600-56528800	Strong transcription	Brain Cingulate Gyrus	brain
39	chr12:56524600-56536000	Strong transcription	Adipose Nuclei	Adipose
40	chr12:56524600-56536000	Strong transcription	Lung	lung
41	chr12:56524600-56536600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr12:56524600-56537400	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:56524600-56537600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
44	chr12:56524600-56538000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:56524600-56538600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:56524600-56538800	Strong transcription	Fetal Brain Female	brain
47	chr12:56524600-56539000	Strong transcription	Colon Smooth Muscle	Colon
48	chr12:56524600-56539200	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr12:56524600-56539400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:56524600-56539400	Strong transcription	HSMM	muscle

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