Variant report

Variant	rs55995758
Chromosome Location	chr16:12118069-12118070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:12117802..12119808-chr16:12131237..12134162,2	MCF-7	breast:
2	chr16:12068828..12072359-chr16:12117169..12120715,5	MCF-7	breast:
3	chr16:12116481..12118828-chr16:12130919..12132635,2	MCF-7	breast:
4	chr16:12007062..12009110-chr16:12118067..12119851,2	K562	blood:
5	chr16:12117021..12119619-chr17:59487538..59489759,2	MCF-7	breast:
6	chr16:12104065..12105673-chr16:12116123..12118604,2	MCF-7	breast:
7	chr16:12007751..12010680-chr16:12116935..12120021,3	MCF-7	breast:
8	chr16:12069225..12071797-chr16:12115611..12118590,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000103342	Chromatin interaction
ENSG00000260488	Chromatin interaction
ENSG00000234719	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000266163	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11075042	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11641950	0.83[EUR][1000 genomes]
rs11859105	0.89[ASN][1000 genomes]
rs11859378	0.85[ASN][1000 genomes]
rs11859602	0.89[ASN][1000 genomes]
rs11859670	0.85[ASN][1000 genomes]
rs11859801	0.89[ASN][1000 genomes]
rs11862031	0.89[ASN][1000 genomes]
rs11862467	0.82[EUR][1000 genomes]
rs11863344	0.89[ASN][1000 genomes]
rs11863772	0.89[ASN][1000 genomes]
rs11864775	0.85[ASN][1000 genomes]
rs11865036	0.89[ASN][1000 genomes]
rs11865132	0.89[ASN][1000 genomes]
rs11865547	0.85[ASN][1000 genomes]
rs2257492	0.93[ASN][1000 genomes]
rs2865105	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34321532	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34701893	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35106911	0.89[ASN][1000 genomes]
rs3826097	0.85[ASN][1000 genomes]
rs3826098	0.89[ASN][1000 genomes]
rs3844112	0.83[EUR][1000 genomes]
rs3851006	0.89[ASN][1000 genomes]
rs3851007	0.89[ASN][1000 genomes]
rs3862465	0.89[ASN][1000 genomes]
rs459292	0.89[ASN][1000 genomes]
rs55719789	0.89[ASN][1000 genomes]
rs55788618	0.89[ASN][1000 genomes]
rs55845335	0.82[ASN][1000 genomes]
rs56166842	0.85[ASN][1000 genomes]
rs56325311	0.85[ASN][1000 genomes]
rs62037727	0.93[ASN][1000 genomes]
rs62037728	0.89[ASN][1000 genomes]
rs62037734	0.85[ASN][1000 genomes]
rs62037735	0.85[ASN][1000 genomes]
rs62037736	0.89[ASN][1000 genomes]
rs62037739	0.89[ASN][1000 genomes]
rs62037740	0.89[ASN][1000 genomes]
rs62037741	0.85[ASN][1000 genomes]
rs7184186	0.89[ASN][1000 genomes]
rs7186759	0.89[ASN][1000 genomes]
rs7192463	0.89[ASN][1000 genomes]
rs7196418	0.89[ASN][1000 genomes]
rs7197059	0.82[EUR][1000 genomes]
rs7200173	0.85[ASN][1000 genomes]
rs7202235	0.89[ASN][1000 genomes]
rs7202328	0.85[ASN][1000 genomes]
rs7202330	0.89[ASN][1000 genomes]
rs7202375	0.89[ASN][1000 genomes]
rs7206768	0.80[EUR][1000 genomes]
rs72784623	0.89[ASN][1000 genomes]
rs72784632	0.85[ASN][1000 genomes]
rs8044821	0.89[ASN][1000 genomes]
rs8044943	0.83[EUR][1000 genomes]
rs8045202	0.85[ASN][1000 genomes]
rs8050827	0.84[AMR][1000 genomes]
rs8051012	0.83[EUR][1000 genomes]
rs8051298	0.89[ASN][1000 genomes]
rs8052866	0.89[ASN][1000 genomes]
rs8057116	0.89[ASN][1000 genomes]
rs8060439	0.82[EUR][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	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs55995758	RP11-166B2.1	cis	Artery Tibial	GTEx
rs55995758	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs55995758	RP11-166B2.1	cis	Whole Blood	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
3	chr16:12085400-12118200	Weak transcription	Esophagus	oesophagus
4	chr16:12098400-12136000	Weak transcription	Fetal Stomach	stomach
5	chr16:12098600-12118200	Weak transcription	Pancreas	Pancrea
6	chr16:12099400-12118400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr16:12099600-12135200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr16:12099600-12141200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr16:12101800-12121400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr16:12101800-12123600	Weak transcription	Lung	lung
11	chr16:12101800-12129800	Weak transcription	Aorta	Aorta
12	chr16:12102000-12124200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr16:12105000-12120600	Weak transcription	Brain Substantia Nigra	brain
14	chr16:12105200-12142200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr16:12105400-12120800	Weak transcription	Fetal Thymus	thymus
16	chr16:12105800-12120800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr16:12105800-12124200	Weak transcription	Primary T cells from cord blood	blood
18	chr16:12108400-12119400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr16:12108600-12128400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr16:12109800-12118200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr16:12109800-12124200	Weak transcription	Left Ventricle	heart
22	chr16:12109800-12142200	Weak transcription	Gastric	stomach
23	chr16:12110000-12118400	Enhancers	Primary B cells from peripheral blood	blood
24	chr16:12110400-12118200	Enhancers	Primary B cells from cord blood	blood
25	chr16:12110600-12119600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr16:12110800-12119400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr16:12111000-12119200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr16:12111000-12119400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr16:12112000-12118400	Weak transcription	NHDF-Ad	bronchial
30	chr16:12112000-12120800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:12112000-12124200	Weak transcription	HSMMtube	muscle
32	chr16:12112000-12129200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr16:12112000-12142200	Weak transcription	NHLF	lung
34	chr16:12112000-12144000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr16:12113200-12129200	Weak transcription	Ovary	ovary
36	chr16:12113400-12118200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr16:12114200-12120800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr16:12115200-12118600	Genic enhancers	GM12878-XiMat	blood
39	chr16:12115200-12140600	Weak transcription	Thymus	Thymus
40	chr16:12116000-12118400	Weak transcription	Adipose Nuclei	Adipose
41	chr16:12116200-12141000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr16:12116600-12120800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr16:12116800-12120000	Weak transcription	Brain Hippocampus Middle	brain
44	chr16:12116800-12129600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr16:12116800-12130800	Weak transcription	Fetal Kidney	kidney
46	chr16:12117200-12140400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr16:12117400-12118600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr16:12117600-12120200	Weak transcription	Fetal Brain Female	brain
50	chr16:12117800-12119800	Enhancers	HepG2	liver

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