Variant report

Variant	rs1342059
Chromosome Location	chr6:142621947-142621948
allele	C/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	GATA2	chr6:142621672-142622536	HUVEC	blood vessel:	n/a	chr6:142622241-142622249 chr6:142621769-142621778
2	SMARCC1	chr6:142621664-142623934	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr6:142621828-142622670	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr6:142621261-142624876	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr6:142621379-142624744	HUVEC	blood vessel:	n/a	n/a
6	TCF12	chr6:142621597-142622549	SK-N-SH	brain:	n/a	n/a
7	FOS	chr6:142621739-142622444	MCF10A-Er-Src	breast:	n/a	n/a
8	RAD21	chr6:142621821-142622405	Hela-S3	cervix:	n/a	n/a
9	FOS	chr6:142621765-142622263	HUVEC	blood vessel:	n/a	n/a
10	USF2	chr6:142621760-142622463	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:142621846-142622277	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr6:142621686-142623227	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr6:142621656-142624313	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr6:142621895-142623437	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr6:142621685-142623763	HUVEC	blood vessel:	n/a	n/a
16	MAX	chr6:142621679-142624627	HepG2	liver:	n/a	chr6:142622591-142622601
17	SMC3	chr6:142621618-142622467	Hela-S3	cervix:	n/a	n/a
18	NFIC	chr6:142621638-142622544	SK-N-SH	brain:	n/a	n/a
19	MAX	chr6:142621741-142624053	HCT-116	colon:	n/a	chr6:142622591-142622601
20	FOXA2	chr6:142621749-142624322	HepG2	liver:	n/a	n/a
21	GATA3	chr6:142621495-142622713	SK-N-SH	brain:	n/a	chr6:142622241-142622249 chr6:142621769-142621778
22	CHD2	chr6:142621589-142622479	Hela-S3	cervix:	n/a	n/a
23	STAT3	chr6:142621534-142622429	MCF10A-Er-Src	breast:	n/a	n/a
24	MAX	chr6:142621907-142622673	A549	lung:	n/a	chr6:142622591-142622601
25	POLR2A	chr6:142621374-142624737	HUVEC	blood vessel:	n/a	n/a
26	E2F4	chr6:142621857-142622165	MCF10A-Er-Src	breast:	n/a	n/a
27	PBX3	chr6:142621686-142622495	SK-N-SH	brain:	n/a	n/a
28	FOSL2	chr6:142621689-142622421	A549	lung:	n/a	n/a
29	SIN3AK20	chr6:142621856-142622436	A549	lung:	n/a	n/a
30	MAX	chr6:142621905-142622551	MCF-7	breast:	n/a	n/a
31	POLR2A	chr6:142621944-142622606	PFSK-1	brain:	n/a	n/a
32	MXI1	chr6:142621862-142622501	Hela-S3	cervix:	n/a	n/a
33	FOS	chr6:142621658-142622356	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr6:142621830-142622048	MCF10A-Er-Src	breast:	n/a	n/a
35	SP1	chr6:142621750-142622467	A549	lung:	n/a	n/a
36	EP300	chr6:142621712-142622240	SK-N-SH_RA	brain:	n/a	n/a
37	MAX	chr6:142621554-142623878	Hela-S3	cervix:	n/a	chr6:142622591-142622601
38	EP300	chr6:142621593-142622518	A549	lung:	n/a	n/a
39	PBX3	chr6:142621568-142622578	SK-N-SH	brain:	n/a	n/a
40	MYBL2	chr6:142621734-142624511	HepG2	liver:	n/a	n/a
41	POLR2A	chr6:142621926-142622631	HCT-116	colon:	n/a	n/a
42	GATA3	chr6:142621545-142624171	A549	lung:	n/a	chr6:142622241-142622249 chr6:142621769-142621778
43	MAX	chr6:142621389-142624658	A549	lung:	n/a	chr6:142622591-142622601
44	SIN3AK20	chr6:142621709-142624147	MCF-7	breast:	n/a	n/a
45	POLR2A	chr6:142621573-142623970	Hela-S3	cervix:	n/a	n/a
46	GTF2F1	chr6:142621756-142622481	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr6:142620820-142625014	PANC-1	pancreas:	n/a	n/a
48	TCF12	chr6:142621556-142622747	SK-N-SH	brain:	n/a	chr6:142622665-142622675
49	STAT3	chr6:142621845-142622445	Hela-S3	cervix:	n/a	n/a
50	FOS	chr6:142621404-142622372	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142616863..142618821-chr6:142620050..142622053,2	K562	blood:

Variant related genes	Relation type
GPR126	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1475770	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225625	1.00[JPT][hapmap]
rs225626	1.00[JPT][hapmap]
rs225627	1.00[JPT][hapmap]
rs225638	1.00[JPT][hapmap]
rs225647	1.00[JPT][hapmap]
rs225649	1.00[JPT][hapmap]
rs225694	1.00[JPT][hapmap]
rs225711	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72986537	1.00[AFR][1000 genomes];1.00[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1029666	chr6:142594099-142643084	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv275340	chr6:142620405-142624568	Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142618800-142622000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:142619200-142622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:142619400-142622000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:142619400-142622000	Enhancers	Placenta	Placenta
5	chr6:142619600-142622200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:142619600-142622200	Weak transcription	NHDF-Ad	bronchial
7	chr6:142619800-142622000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:142619800-142622000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:142619800-142622000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:142619800-142622000	Weak transcription	NH-A	brain
11	chr6:142620000-142622000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:142620000-142622200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:142620400-142622000	Weak transcription	HSMMtube	muscle
14	chr6:142620400-142622200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:142620600-142622200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:142621400-142622000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:142621400-142622000	Enhancers	Duodenum Mucosa	Duodenum
18	chr6:142621400-142622400	Flanking Active TSS	Hela-S3	cervix
19	chr6:142621600-142622000	Flanking Active TSS	NHEK	skin
20	chr6:142621600-142622200	Flanking Active TSS	A549	lung
21	chr6:142621600-142622200	Flanking Active TSS	HepG2	liver
22	chr6:142621600-142622400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:142621600-142622600	Flanking Active TSS	Liver	Liver
24	chr6:142621600-142622600	Flanking Active TSS	HUVEC	blood vessel
25	chr6:142621800-142622000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:142621800-142622000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr6:142621800-142622000	Enhancers	Primary hematopoietic stem cells	blood
28	chr6:142621800-142622000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:142621800-142622000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:142621800-142622000	Enhancers	Fetal Brain Male	brain
31	chr6:142621800-142622000	Enhancers	Fetal Intestine Large	intestine
32	chr6:142621800-142622000	Enhancers	Fetal Intestine Small	intestine
33	chr6:142621800-142622000	Enhancers	Stomach Mucosa	stomach
34	chr6:142621800-142622000	Enhancers	HSMM	muscle
35	chr6:142621800-142622000	Enhancers	NHLF	lung
36	chr6:142621800-142622000	Enhancers	Osteobl	bone
37	chr6:142621800-142622200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:142621800-142622200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:142621800-142622400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:142621800-142622400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:142621800-142622400	Flanking Active TSS	Fetal Lung	lung
42	chr6:142621800-142622400	Flanking Active TSS	HMEC	breast
43	chr6:142621800-142622600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:142621800-142622600	Enhancers	Fetal Heart	heart
45	chr6:142621800-142623000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:142621800-142625600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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