Variant report

Variant	rs12041620
Chromosome Location	chr1:180492752-180492753
allele	A/C
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	CEBPB	chr1:180492602-180492794	K562	blood:	n/a	chr1:180492680-180492691
2	CEBPB	chr1:180492612-180492830	A549	lung:	n/a	chr1:180492680-180492691
3	CEBPB	chr1:180492528-180492819	HepG2	liver:	n/a	chr1:180492680-180492691
4	CEBPB	chr1:180492531-180492783	IMR90	lung:	n/a	chr1:180492680-180492691
5	POLR2A	chr1:180492595-180492800	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180491628..180493840-chr1:180599404..180602125,2	MCF-7	breast:
2	chr1:180472964..180474571-chr1:180490356..180493108,2	MCF-7	breast:
3	chr1:180470877..180472880-chr1:180490627..180493125,2	K562	blood:
4	chr1:180491568..180494207-chr1:180499661..180501962,2	MCF-7	breast:
5	chr1:180468948..180471810-chr1:180491211..180493029,2	MCF-7	breast:
6	chr1:180491722..180497520-chr1:180497939..180503107,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206905	TF binding region
ENSG00000135847	Chromatin interaction
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10753216	0.82[ASN][1000 genomes]
rs10914018	0.82[ASN][1000 genomes]
rs12039331	0.84[ASN][1000 genomes]
rs12565492	0.82[ASN][1000 genomes]
rs1416823	1.00[ASN][1000 genomes]
rs16856086	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16856087	0.96[ASN][1000 genomes]
rs1890731	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1970400	0.88[EUR][1000 genomes]
rs3806300	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3806301	0.86[EUR][1000 genomes]
rs6425641	0.87[EUR][1000 genomes]
rs6425644	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425645	0.94[ASN][1000 genomes]
rs6687442	0.88[EUR][1000 genomes]
rs6687549	0.88[EUR][1000 genomes]
rs6699076	0.93[ASN][1000 genomes]
rs6699585	0.88[EUR][1000 genomes]
rs6704334	0.88[EUR][1000 genomes]
rs6704437	0.88[EUR][1000 genomes]
rs72720915	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72720917	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72720922	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521151	0.93[EUR][1000 genomes]
rs9701037	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9726041	0.88[EUR][1000 genomes]
rs9730180	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
3	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180486000-180493400	Weak transcription	Fetal Stomach	stomach
2	chr1:180486000-180499400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:180486400-180493800	Weak transcription	Fetal Lung	lung
4	chr1:180488000-180500400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:180488600-180497000	Enhancers	Placenta	Placenta
6	chr1:180489400-180494400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:180489800-180494400	Weak transcription	HUVEC	blood vessel
8	chr1:180490600-180492800	Enhancers	HMEC	breast
9	chr1:180490800-180493800	Weak transcription	Lung	lung
10	chr1:180491000-180499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:180491400-180493000	Enhancers	Hela-S3	cervix
12	chr1:180491400-180493400	Weak transcription	Right Ventricle	heart
13	chr1:180491400-180493800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:180491400-180494000	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:180491400-180496200	Weak transcription	A549	lung
16	chr1:180491400-180496400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:180491400-180499400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:180491600-180493200	Weak transcription	Right Atrium	heart
19	chr1:180491600-180511200	Weak transcription	Psoas Muscle	Psoas
20	chr1:180492000-180494000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:180492000-180494000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:180492000-180494800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:180492000-180495400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:180492000-180495400	Weak transcription	K562	blood
25	chr1:180492200-180493400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:180492200-180494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:180492200-180494000	Weak transcription	Fetal Heart	heart
28	chr1:180492200-180494600	Weak transcription	Fetal Intestine Small	intestine
29	chr1:180492200-180494800	Weak transcription	Fetal Intestine Large	intestine
30	chr1:180492200-180495800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:180492400-180493400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:180492400-180493800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:180492400-180496400	Weak transcription	NHEK	skin
34	chr1:180492400-180499400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:180492400-180503000	Weak transcription	Pancreas	Pancrea
36	chr1:180492600-180493400	Weak transcription	Left Ventricle	heart
37	chr1:180492600-180493800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:180492600-180495400	Weak transcription	HepG2	liver
39	chr1:180492600-180498000	Weak transcription	HSMMtube	muscle

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