Variant report

Variant	rs4899139
Chromosome Location	chr14:39483911-39483912
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39410789..39411608-chr14:39483894..39485313,6	MCF-7	breast:
2	chr14:39480586..39482188-chr14:39482483..39485186,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10132034	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10132953	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10149829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11157046	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12434607	0.82[EUR][1000 genomes]
rs12895329	0.96[EUR][1000 genomes]
rs175341	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1950509	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1955917	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964842	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2038357	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2064959	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2180214	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2180217	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2180792	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2415525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs3899404	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4616209	0.85[EUR][1000 genomes]
rs4899125	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4899126	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4899140	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902272	1.00[CHD][hapmap]
rs4902294	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902402	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs4902419	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6571886	0.80[ASN][1000 genomes]
rs6571888	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6571889	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6571890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6571891	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6571894	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6571896	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7143480	0.80[ASN][1000 genomes]
rs7147760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7154585	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7157204	0.81[AMR][1000 genomes]
rs761804	0.85[EUR][1000 genomes]
rs761806	0.87[EUR][1000 genomes]
rs761807	0.87[EUR][1000 genomes]
rs8003194	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8003485	0.87[EUR][1000 genomes]
rs8003807	0.85[EUR][1000 genomes]
rs8004480	0.80[ASN][1000 genomes]
rs8011855	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8012178	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8014021	0.93[ASN][1000 genomes]
rs8014255	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs8014677	0.83[EUR][1000 genomes]
rs9322993	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9671927	0.87[EUR][1000 genomes]
rs970623	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39463600-39495200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr14:39464800-39492600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr14:39465600-39498200	Weak transcription	NH-A	brain
4	chr14:39469200-39497400	Weak transcription	HSMM	muscle
5	chr14:39473400-39498800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:39473800-39485400	Weak transcription	HSMMtube	muscle
7	chr14:39475000-39485600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr14:39479000-39493000	Weak transcription	A549	lung
9	chr14:39479600-39498000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr14:39479800-39492800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr14:39480200-39499000	Weak transcription	NHDF-Ad	bronchial
12	chr14:39480400-39484000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr14:39481200-39486400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr14:39481200-39492600	Weak transcription	Fetal Intestine Small	intestine
15	chr14:39482200-39486000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr14:39482200-39495000	Weak transcription	HUVEC	blood vessel
17	chr14:39482400-39485800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr14:39482800-39499200	Weak transcription	Right Ventricle	heart
19	chr14:39483000-39485200	Weak transcription	Fetal Heart	heart
20	chr14:39483000-39486400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr14:39483200-39484000	Weak transcription	Brain Hippocampus Middle	brain
22	chr14:39483400-39484600	Enhancers	HepG2	liver
23	chr14:39483400-39485200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr14:39483600-39484800	Weak transcription	Liver	Liver
25	chr14:39483600-39485400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr14:39483600-39486400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr14:39483800-39485200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr14:39483800-39485200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:39483800-39492600	Weak transcription	Osteobl	bone

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