Variant report

Variant	rs55686038
Chromosome Location	chr3:156513635-156513636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156511443..156514297-chr3:156542568..156546057,3	K562	blood:
2	chr3:156512318..156515749-chr3:156532342..156535718,6	MCF-7	breast:
3	chr3:156511539..156515670-chr3:156534047..156537990,6	MCF-7	breast:
4	chr3:156513155..156515198-chr3:156521079..156523360,2	K562	blood:

Variant related genes	Relation type
ENSG00000240875	Chromatin interaction
ENSG00000197980	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10513495	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12636629	0.92[EUR][1000 genomes]
rs1367312	0.90[EUR][1000 genomes]
rs1529581	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17373227	0.88[EUR][1000 genomes]
rs344004	0.93[AMR][1000 genomes]
rs41366145	0.92[EUR][1000 genomes]
rs4364127	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748213	0.92[ASN][1000 genomes]
rs56128116	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56152727	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56245561	0.87[EUR][1000 genomes]
rs56354026	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56357051	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56836190	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56960846	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57483705	0.92[EUR][1000 genomes]
rs58263861	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58822703	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59689193	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60032002	1.00[ASN][1000 genomes]
rs60178381	0.82[ASN][1000 genomes]
rs73013957	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73019737	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019749	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs891463	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919520	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs55686038	LINC00886	cis	Thyroid	GTEx
rs55686038	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs55686038	LINC00886	cis	Artery Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156502800-156528400	Weak transcription	Esophagus	oesophagus
2	chr3:156502800-156529000	Weak transcription	Liver	Liver
3	chr3:156504200-156516400	Weak transcription	Primary B cells from cord blood	blood
4	chr3:156510000-156513800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr3:156510000-156513800	Weak transcription	Fetal Intestine Small	intestine
6	chr3:156510000-156513800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:156510800-156514000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:156511000-156519600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:156511200-156513800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:156511200-156513800	Weak transcription	HUVEC	blood vessel
11	chr3:156511200-156515000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:156511200-156516600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:156511200-156529000	Weak transcription	Primary T cells from cord blood	blood
14	chr3:156511400-156513800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:156511400-156513800	Weak transcription	GM12878-XiMat	blood
16	chr3:156511400-156513800	Weak transcription	NHEK	skin
17	chr3:156511400-156518800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:156511400-156530400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:156511600-156513800	Weak transcription	Brain Substantia Nigra	brain
20	chr3:156511600-156514000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:156511600-156519600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:156511800-156514000	Weak transcription	HSMM	muscle
23	chr3:156512600-156513800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:156512600-156513800	Weak transcription	Osteobl	bone
25	chr3:156513200-156514400	Enhancers	NHDF-Ad	bronchial
26	chr3:156513400-156514000	Enhancers	Stomach Mucosa	stomach
27	chr3:156513400-156514200	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr3:156513400-156514200	Enhancers	A549	lung
29	chr3:156513400-156514400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:156513400-156514400	Enhancers	HMEC	breast
31	chr3:156513600-156513800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:156513600-156513800	Flanking Active TSS	HepG2	liver
33	chr3:156513600-156514200	Enhancers	Hela-S3	cervix
34	chr3:156513600-156514400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr3:156513600-156515200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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