Variant report

Variant	rs12492968
Chromosome Location	chr3:156541837-156541838
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	CTCF	chr3:156541760-156541910	GM12865	blood:	n/a	n/a
2	CTCF	chr3:156541820-156541970	HBMEC	blood vessel:	n/a	n/a
3	CTCF	chr3:156541700-156541850	GM12864	blood:	n/a	n/a
4	CTCF	chr3:156541780-156541930	GM12873	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156268894..156273100-chr3:156541711..156545313,4	MCF-7	breast:
2	chr3:156527592..156531932-chr3:156540848..156546879,8	MCF-7	breast:

Variant related genes	Relation type
LEKR1	TF binding region
ENSG00000230457	Chromatin interaction
ENSG00000114850	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10936037	0.80[EUR][1000 genomes]
rs10936038	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11707914	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11711674	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12107178	0.82[ASN][1000 genomes]
rs12629380	0.81[EUR][1000 genomes]
rs13086516	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13097325	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1560415	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1560416	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17382070	0.82[EUR][1000 genomes]
rs2060015	0.83[EUR][1000 genomes]
rs2321290	0.82[EUR][1000 genomes]
rs34667021	0.81[EUR][1000 genomes]
rs3910072	0.83[EUR][1000 genomes]
rs4098	0.85[ASN][1000 genomes]
rs4680305	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7623691	0.88[ASN][1000 genomes]
rs7638625	0.84[EUR][1000 genomes]
rs9812895	0.82[EUR][1000 genomes]
rs9818684	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818780	0.87[ASN][1000 genomes]
rs9820830	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9837271	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9847187	0.83[EUR][1000 genomes]
rs9859058	0.90[ASN][1000 genomes]
rs9867621	0.81[EUR][1000 genomes]
rs9867857	0.85[ASN][1000 genomes]
rs9871817	0.82[EUR][1000 genomes]
rs9876010	0.83[EUR][1000 genomes]
rs9878566	0.87[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
rs12492968	LINC00886	cis	lung	GTEx
rs12492968	LINC00886	cis	Adipose Subcutaneous	GTEx
rs12492968	LINC00886	cis	Artery Aorta	GTEx
rs12492968	LINC00886	cis	Stomach	GTEx
rs12492968	LINC00886	cis	Muscle Skeletal	GTEx
rs12492968	LINC00886	cis	Esophagus Muscularis	GTEx
rs12492968	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs12492968	LINC00886	cis	Esophagus Mucosa	GTEx
rs12492968	LINC00886	cis	Thyroid	GTEx
rs12492968	LINC00886	cis	Artery Tibial	GTEx
rs12492968	LINC00886	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156535400-156543400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:156536200-156543200	Weak transcription	Fetal Kidney	kidney
3	chr3:156536400-156542400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:156536400-156542400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:156536400-156543000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:156536400-156543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:156536400-156543200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:156536400-156543200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:156536400-156543200	Weak transcription	Thymus	Thymus
10	chr3:156537000-156543200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:156537000-156543400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:156537000-156543400	Weak transcription	Liver	Liver
13	chr3:156537000-156543600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:156537000-156543600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:156537200-156542600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:156537600-156542400	Weak transcription	K562	blood
17	chr3:156538000-156543400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:156538600-156543200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:156538600-156543400	Weak transcription	NHLF	lung
20	chr3:156538800-156542000	Weak transcription	NHEK	skin
21	chr3:156538800-156542200	Weak transcription	A549	lung
22	chr3:156538800-156543200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:156538800-156543200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:156538800-156543200	Weak transcription	NHDF-Ad	bronchial
25	chr3:156538800-156543400	Weak transcription	HSMMtube	muscle
26	chr3:156539000-156542000	Weak transcription	Stomach Mucosa	stomach
27	chr3:156539000-156542400	Weak transcription	Hela-S3	cervix
28	chr3:156539000-156543200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:156539000-156543200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:156539000-156543200	Weak transcription	HMEC	breast
31	chr3:156539000-156543200	Weak transcription	HSMM	muscle
32	chr3:156539000-156543200	Weak transcription	HUVEC	blood vessel
33	chr3:156539000-156543200	Weak transcription	Osteobl	bone
34	chr3:156539000-156543400	Weak transcription	NH-A	brain
35	chr3:156539200-156543200	Weak transcription	GM12878-XiMat	blood
36	chr3:156539200-156543400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:156540800-156542200	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:156541400-156542200	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr3:156541400-156542200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:156541600-156543000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr3:156541800-156542400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:156541800-156542400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:156541800-156543200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:156541800-156543400	Enhancers	Fetal Intestine Large	intestine
45	chr3:156541800-156543600	Enhancers	Fetal Intestine Small	intestine
46	chr3:156541800-156543800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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