Variant report

Variant	rs2701641
Chromosome Location	chr12:120691424-120691425
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	RUNX3	chr12:120691122-120691570	GM12878	blood:	n/a	n/a
2	FOS	chr12:120691227-120691493	MCF10A-Er-Src	breast:	n/a	n/a
3	SPI1	chr12:120691245-120691554	HL-60	blood:	n/a	n/a
4	FOS	chr12:120691192-120691524	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:120691313-120691661	PANC-1	pancreas:	n/a	n/a
6	CEBPB	chr12:120691343-120691452	A549	lung:	n/a	chr12:120691345-120691356
7	STAT3	chr12:120691218-120691502	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr12:120691295-120691486	HepG2	liver:	n/a	chr12:120691345-120691356
9	STAT3	chr12:120691153-120691555	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr12:120691352-120691490	H1-hESC	embryonic stem cell:	n/a	n/a
11	MYC	chr12:120691273-120691464	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr12:120691165-120691542	MCF10A-Er-Src	breast:	n/a	n/a
13	CEBPB	chr12:120691205-120691523	Hela-S3	cervix:	n/a	chr12:120691345-120691356
14	RUNX3	chr12:120691221-120691491	GM12878	blood:	n/a	n/a
15	ATF3	chr12:120691276-120691455	K562	blood:	n/a	n/a
16	CEBPB	chr12:120691218-120691534	K562	blood:	n/a	chr12:120691345-120691356
17	FOS	chr12:120691232-120691502	MCF10A-Er-Src	breast:	n/a	n/a
18	CEBPB	chr12:120691200-120691538	K562	blood:	n/a	chr12:120691345-120691356

No.	Distal block	Cell Line	Cell type
1	chr12:120690051..120707499-chr12:120720410..120732530,91	MCF-7	breast:
2	chr12:120684404..120691478-chr12:120697984..120705218,14	MCF-7	breast:
3	chr12:120631592..120634206-chr12:120689863..120692098,2	K562	blood:
4	chr12:120687814..120689753-chr12:120689837..120693195,3	K562	blood:
5	chr12:120685214..120692467-chr12:120727115..120732311,17	K562	blood:
6	chr12:120685626..120692224-chr12:120727115..120732105,16	K562	blood:
7	chr12:120690570..120692197-chr12:120693845..120695408,2	K562	blood:
8	chr12:120687678..120692479-chr12:120701581..120703521,4	K562	blood:

Variant related genes	Relation type
PXN	TF binding region
ENSG00000089159	Chromatin interaction
ENSG00000089154	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1151821	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1151822	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1151823	1.00[ASN][1000 genomes]
rs1151826	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs1151828	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1151833	1.00[ASN][1000 genomes]
rs1151835	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1151836	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1166788	1.00[ASN][1000 genomes]
rs1166789	0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1179386	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12322327	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12580333	0.95[ASN][1000 genomes]
rs12580868	0.90[CHB][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap]
rs12582981	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1632619	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1634820	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16950044	0.89[CHB][hapmap]
rs16950047	0.89[CHB][hapmap]
rs2239207	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2283363	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs3847967	0.89[CHB][hapmap]
rs3847968	1.00[CHB][hapmap]
rs58777856	0.95[ASN][1000 genomes]
rs58919380	1.00[ASN][1000 genomes]
rs60134107	1.00[ASN][1000 genomes]
rs60282545	0.95[ASN][1000 genomes]
rs61633133	1.00[ASN][1000 genomes]
rs71541558	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
4	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120665200-120692000	Enhancers	Placenta	Placenta
2	chr12:120676400-120699400	Weak transcription	Aorta	Aorta
3	chr12:120683200-120694800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:120683200-120695200	Weak transcription	Fetal Brain Male	brain
5	chr12:120684000-120692000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:120686000-120700200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:120686600-120692800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr12:120686600-120693200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:120686600-120695000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:120687600-120693200	Genic enhancers	NHEK	skin
11	chr12:120688000-120692800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:120688000-120693000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:120688000-120694000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:120688000-120694000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:120688000-120694200	Weak transcription	Brain Angular Gyrus	brain
16	chr12:120688000-120694200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:120688000-120695200	Weak transcription	Gastric	stomach
18	chr12:120688200-120692000	Enhancers	Primary B cells from peripheral blood	blood
19	chr12:120688200-120694800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:120688200-120695000	Weak transcription	Liver	Liver
21	chr12:120688400-120692000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:120688400-120692200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:120688400-120692800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:120688400-120694000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:120688400-120694200	Weak transcription	Pancreas	Pancrea
26	chr12:120688400-120694400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:120688400-120694800	Weak transcription	Esophagus	oesophagus
28	chr12:120688600-120692800	Weak transcription	Fetal Lung	lung
29	chr12:120688600-120694000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:120688600-120694000	Weak transcription	Brain Substantia Nigra	brain
31	chr12:120688600-120694200	Weak transcription	Fetal Heart	heart
32	chr12:120688600-120694200	Weak transcription	Stomach Mucosa	stomach
33	chr12:120688600-120700200	Weak transcription	Fetal Kidney	kidney
34	chr12:120688800-120694000	Weak transcription	Brain Anterior Caudate	brain
35	chr12:120688800-120694000	Weak transcription	Right Ventricle	heart
36	chr12:120688800-120694200	Weak transcription	HepG2	liver
37	chr12:120689400-120691600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr12:120689400-120691600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr12:120689400-120692000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr12:120689400-120692200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:120689400-120692200	Enhancers	GM12878-XiMat	blood
42	chr12:120689400-120692400	Weak transcription	Fetal Stomach	stomach
43	chr12:120689400-120692600	Enhancers	Primary hematopoietic stem cells	blood
44	chr12:120689400-120693200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:120689600-120691600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:120689600-120691600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr12:120689600-120691600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr12:120689600-120691600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:120689600-120691600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr12:120689600-120691800	Enhancers	Placenta Amnion	Placenta Amnion

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