Variant report

Variant	rs12492804
Chromosome Location	chr3:156532145-156532146
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:156532052-156532466	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:156532103-156532462	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr3:156532117-156532441	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr3:156532122-156532381	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr3:156532009-156532468	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr3:156532031-156532447	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr3:156532119-156532453	MCF10A-Er-Src	breast:	n/a	n/a
8	E2F4	chr3:156532105-156532337	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr3:156532072-156532401	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156391553..156394223-chr3:156530300..156532629,2	K562	blood:
2	chr3:156530292..156533416-chr3:156536221..156538650,3	MCF-7	breast:
3	chr3:156473925..156475746-chr3:156530904..156533375,2	MCF-7	breast:
4	chr3:156522791..156525819-chr3:156530782..156532939,3	MCF-7	breast:
5	chr3:156270408..156273288-chr3:156530835..156533779,2	MCF-7	breast:
6	chr3:156531546..156534096-chr3:156793933..156795686,2	MCF-7	breast:
7	chr3:156400050..156402088-chr3:156531912..156534314,2	MCF-7	breast:
8	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
9	chr3:156497492..156500885-chr3:156532144..156534276,3	K562	blood:
10	chr3:156402796..156405445-chr3:156530779..156533531,2	MCF-7	breast:
11	chr3:156530884..156532609-chr3:156891985..156894851,2	MCF-7	breast:
12	chr3:156530216..156532271-chr3:156875722..156877801,2	MCF-7	breast:
13	chr3:156530706..156532325-chr3:156799131..156800812,2	MCF-7	breast:
14	chr3:156517343..156519280-chr3:156530527..156533564,3	MCF-7	breast:
15	chr3:156256323..156258307-chr3:156531885..156534419,2	MCF-7	breast:
16	chr3:156389670..156395497-chr3:156530360..156537244,22	MCF-7	breast:

No data

Variant related genes	Relation type
PA2G4P4	TF binding region
ENSG00000243176	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000241544	Chromatin interaction
ENSG00000114850	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10936037	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10936038	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711674	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717133	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12497539	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072896	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13086516	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13097325	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560415	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560416	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1835372	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680305	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59717073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6776157	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7641929	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818684	0.81[AMR][1000 genomes]
rs9820830	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9837271	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842198	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858861	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12492804	LINC00886	cis	Esophagus Mucosa	GTEx
rs12492804	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs12492804	LINC00886	cis	Muscle Skeletal	GTEx
rs12492804	LINC00886	cis	Esophagus Muscularis	GTEx
rs12492804	LINC00886	cis	Artery Tibial	GTEx
rs12492804	LINC00886	cis	Artery Aorta	GTEx
rs12492804	LINC00886	cis	Thyroid	GTEx
rs12492804	LINC00886	cis	Adipose Subcutaneous	GTEx
rs12492804	LINC00886	cis	Stomach	GTEx
rs12492804	LINC00886	cis	lung	GTEx
rs12492804	LINC00886	cis	Nerve Tibial	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156527200-156533200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:156527400-156533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:156527800-156533000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:156527800-156533800	Enhancers	HMEC	breast
5	chr3:156528200-156533600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:156528400-156532800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:156529200-156533600	Weak transcription	Primary B cells from cord blood	blood
8	chr3:156529400-156533400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:156529600-156532400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:156529600-156533600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:156529800-156533600	Weak transcription	Fetal Heart	heart
12	chr3:156530600-156533400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:156530600-156533600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:156530600-156533800	Weak transcription	Lung	lung
15	chr3:156530800-156533800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:156530800-156533800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:156530800-156533800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:156530800-156533800	Weak transcription	Left Ventricle	heart
19	chr3:156531000-156532600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:156531000-156533200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:156531000-156533400	Weak transcription	NHLF	lung
22	chr3:156531000-156533600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:156531000-156533600	Weak transcription	HSMMtube	muscle
24	chr3:156531000-156533800	Weak transcription	Right Ventricle	heart
25	chr3:156531000-156533800	Weak transcription	Small Intestine	intestine
26	chr3:156531200-156532400	Enhancers	Hela-S3	cervix
27	chr3:156531200-156532800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:156531200-156533000	Weak transcription	Fetal Intestine Large	intestine
29	chr3:156531200-156533200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:156531200-156533400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr3:156531200-156533400	Weak transcription	HepG2	liver
32	chr3:156531200-156533400	Weak transcription	HUVEC	blood vessel
33	chr3:156531200-156533400	Weak transcription	NHDF-Ad	bronchial
34	chr3:156531200-156533600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:156531200-156533600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:156531200-156533600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:156531200-156533600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:156531200-156533600	Weak transcription	Osteobl	bone
39	chr3:156531200-156533800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:156531200-156533800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:156531200-156533800	Weak transcription	Esophagus	oesophagus
42	chr3:156531200-156533800	Weak transcription	Pancreas	Pancrea
43	chr3:156531200-156533800	Weak transcription	Psoas Muscle	Psoas
44	chr3:156531200-156533800	Weak transcription	Right Atrium	heart
45	chr3:156531200-156533800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:156531200-156533800	Weak transcription	HSMM	muscle
47	chr3:156531200-156534000	Weak transcription	Aorta	Aorta
48	chr3:156531200-156534000	Weak transcription	Gastric	stomach
49	chr3:156531200-156534200	Weak transcription	Stomach Mucosa	stomach
50	chr3:156531400-156533200	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links