Variant report

Variant	rs677254
Chromosome Location	chr18:11949298-11949299
allele	A/G
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	chr18:11947643..11949972-chr18:11979673..11983782,3	MCF-7	breast:
2	chr18:11908313..11910422-chr18:11947484..11949382,3	K562	blood:
3	chr18:11945871..11949775-chr18:11972448..11976477,3	K562	blood:
4	chr18:11944456..11952400-chr18:11978684..11982486,15	K562	blood:
5	chr18:11945775..11953098-chr18:11977697..11982837,16	K562	blood:
6	chr18:11907115..11909589-chr18:11947697..11950690,2	MCF-7	breast:
7	chr18:11946068..11950381-chr18:11979395..11982010,5	MCF-7	breast:
8	chr18:11949109..11951046-chr18:11952725..11954944,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000141401	Chromatin interaction
ENSG00000273141	Chromatin interaction
ENSG00000154889	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12956610	0.84[YRI][hapmap]
rs16976851	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1811452	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2083810	0.80[ASN][1000 genomes]
rs34478333	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34803006	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35932750	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs581799	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs585176	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs591880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600405	0.80[ASN][1000 genomes]
rs604427	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604453	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs622863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs629550	0.95[CEU][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630068	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs648676	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs649039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs649459	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs650958	0.80[ASN][1000 genomes]
rs651889	0.80[ASN][1000 genomes]
rs661885	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs662981	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs665149	0.80[ASN][1000 genomes]
rs665169	0.80[ASN][1000 genomes]
rs677359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682249	0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs689390	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs694635	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7226885	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7227036	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7504853	0.80[ASN][1000 genomes]
rs8098140	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs9946013	0.80[ASN][1000 genomes]
rs9952563	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9956744	0.80[ASN][1000 genomes]
rs9962395	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
7	nsv1063339	chr18:11909588-11979264	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv576495	chr18:11917410-11986557	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv909385	chr18:11938102-11986557	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
10	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs677254	RP11-820I16.1	cis	Esophagus Muscularis	GTEx
rs677254	RP11-820I16.1	cis	Thyroid	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11947800-11952400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr18:11947800-11954600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr18:11947800-11955000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr18:11948000-11950600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr18:11948000-11951600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr18:11948000-11954400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr18:11948200-11949400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr18:11948200-11949400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr18:11948200-11949400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr18:11948200-11949400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr18:11948200-11949400	Enhancers	Pancreas	Pancrea
12	chr18:11948200-11949800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr18:11948200-11950000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr18:11948200-11950000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr18:11948200-11950000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr18:11948200-11951400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr18:11948200-11951600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr18:11948200-11951600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr18:11948200-11951600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr18:11948200-11951600	Enhancers	K562	blood
21	chr18:11948200-11951800	Weak transcription	Esophagus	oesophagus
22	chr18:11948200-11952200	Weak transcription	NHEK	skin
23	chr18:11948400-11949400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr18:11948400-11949400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr18:11948400-11949400	Enhancers	Stomach Smooth Muscle	stomach
26	chr18:11948400-11949600	Enhancers	A549	lung
27	chr18:11948400-11950800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr18:11948400-11951600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:11948600-11949400	Enhancers	HSMM	muscle
30	chr18:11948600-11949400	Enhancers	NH-A	brain
31	chr18:11948600-11951000	Weak transcription	Fetal Muscle Leg	muscle
32	chr18:11948800-11949400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr18:11948800-11949400	Enhancers	Fetal Lung	lung
34	chr18:11948800-11949400	Enhancers	NHLF	lung
35	chr18:11948800-11949600	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr18:11948800-11949600	Enhancers	HepG2	liver
37	chr18:11948800-11950000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr18:11949000-11949400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr18:11949000-11949400	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr18:11949000-11949400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr18:11949000-11951000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr18:11949000-11951400	Weak transcription	Ovary	ovary
43	chr18:11949000-11951600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr18:11949000-11951600	Weak transcription	Fetal Stomach	stomach
45	chr18:11949000-11951600	Weak transcription	Psoas Muscle	Psoas
46	chr18:11949000-11954000	Weak transcription	HSMMtube	muscle
47	chr18:11949200-11949600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr18:11949200-11949800	Enhancers	Osteobl	bone
49	chr18:11949200-11950800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr18:11949200-11951000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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