Variant report

Variant	rs7972420
Chromosome Location	chr12:57068514-57068515
allele	A/G
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	chr12:57068294-57068576	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57038172..57039913-chr12:57066902..57070182,3	MCF-7	breast:
2	chr12:57057875..57064396-chr12:57067862..57074098,12	K562	blood:
3	chr12:57029198..57030755-chr12:57067875..57070148,2	K562	blood:
4	chr12:57067309..57072885-chr12:57076964..57083697,11	K562	blood:

Variant related genes	Relation type
RN7SL809P	TF binding region
ENSG00000110955	Chromatin interaction
ENSG00000207031	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000076108	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1020848	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747769	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876913	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876914	0.95[ASN][1000 genomes]
rs10876915	0.95[ASN][1000 genomes]
rs10876916	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1107479	0.95[ASN][1000 genomes]
rs11171914	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171916	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171917	0.95[ASN][1000 genomes]
rs11835120	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11837319	0.95[ASN][1000 genomes]
rs12229457	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1465081	0.95[ASN][1000 genomes]
rs1563896	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1563897	0.84[ASN][1000 genomes]
rs1962963	0.83[ASN][1000 genomes]
rs2255074	0.94[ASN][1000 genomes]
rs2290893	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2926740	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2950387	0.89[ASN][1000 genomes]
rs2950388	0.95[ASN][1000 genomes]
rs2950390	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2950393	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2950394	0.95[ASN][1000 genomes]
rs2958123	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958124	0.91[ASN][1000 genomes]
rs2958145	0.95[ASN][1000 genomes]
rs2958146	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958153	0.89[ASN][1000 genomes]
rs2958154	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958155	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36012661	0.95[ASN][1000 genomes]
rs4759028	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67046307	0.95[ASN][1000 genomes]
rs7297289	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7303216	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7315472	0.95[ASN][1000 genomes]
rs73337030	0.95[ASN][1000 genomes]
rs7973157	0.95[ASN][1000 genomes]
rs7975783	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7980378	0.92[ASN][1000 genomes]
rs7980835	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs941207	0.90[ASN][1000 genomes]
rs9634246	0.95[ASN][1000 genomes]
rs9634247	0.93[ASN][1000 genomes]
rs9634277	0.93[ASN][1000 genomes]
rs9989034	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57040400-57069400	Weak transcription	Right Atrium	heart
2	chr12:57052400-57078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:57054200-57069600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:57054800-57075800	Strong transcription	Fetal Thymus	thymus
5	chr12:57054800-57076600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:57055600-57077400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:57056000-57069200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:57058000-57070400	Weak transcription	Psoas Muscle	Psoas
9	chr12:57061400-57075000	Genic enhancers	A549	lung
10	chr12:57064600-57070200	Weak transcription	Fetal Brain Male	brain
11	chr12:57064800-57078000	Weak transcription	HSMMtube	muscle
12	chr12:57064800-57078600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:57065000-57072400	Weak transcription	Brain Angular Gyrus	brain
14	chr12:57065000-57072600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:57065000-57077600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:57065000-57077800	Weak transcription	Stomach Mucosa	stomach
17	chr12:57065200-57069000	Weak transcription	Fetal Muscle Leg	muscle
18	chr12:57065200-57069400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:57065200-57069400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:57065200-57069400	Weak transcription	Gastric	stomach
21	chr12:57065200-57069400	Weak transcription	Ovary	ovary
22	chr12:57065200-57069400	Weak transcription	Right Ventricle	heart
23	chr12:57065200-57069400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:57065200-57069400	Weak transcription	Thymus	Thymus
25	chr12:57065200-57070400	Weak transcription	Spleen	Spleen
26	chr12:57065200-57072400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:57065200-57072600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:57065200-57072600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:57065200-57072600	Weak transcription	Esophagus	oesophagus
30	chr12:57065200-57072600	Weak transcription	Lung	lung
31	chr12:57065200-57074000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:57065200-57074000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:57065200-57074000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:57065200-57078000	Weak transcription	Aorta	Aorta
35	chr12:57065200-57079800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:57065400-57072000	Weak transcription	Colonic Mucosa	Colon
37	chr12:57065400-57073600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:57065400-57077800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr12:57065600-57068800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr12:57065800-57070400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:57065800-57072600	Weak transcription	Brain Substantia Nigra	brain
42	chr12:57065800-57077800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:57066000-57070000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:57066200-57069200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:57066200-57072600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:57066200-57072600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:57066200-57075600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:57066400-57069600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:57066400-57070400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:57066400-57070400	Weak transcription	Pancreas	Pancrea

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