Variant report

Variant	rs6534673
Chromosome Location	chr4:129142166-129142167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10000960	0.80[JPT][hapmap];0.89[YRI][hapmap]
rs10001048	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1001503	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10019554	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10019840	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10026899	0.81[JPT][hapmap]
rs10434053	0.94[AFR][1000 genomes]
rs10518529	0.80[JPT][hapmap]
rs10857128	0.80[JPT][hapmap]
rs10857129	0.80[JPT][hapmap]
rs11098947	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs11098951	0.88[EUR][1000 genomes]
rs11723915	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11727049	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11727305	0.80[JPT][hapmap];0.81[YRI][hapmap]
rs11735810	0.80[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs11737026	0.90[CEU][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes]
rs12498291	0.92[EUR][1000 genomes]
rs12506549	0.80[JPT][hapmap]
rs12508837	0.81[JPT][hapmap]
rs12509092	0.80[JPT][hapmap]
rs12510308	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs12641548	0.80[JPT][hapmap]
rs12645577	0.80[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs12648962	0.82[ASN][1000 genomes]
rs13102049	0.84[JPT][hapmap]
rs13136665	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13137866	0.87[ASN][1000 genomes]
rs13138581	0.84[JPT][hapmap]
rs13139182	0.80[JPT][hapmap]
rs1545711	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16997980	0.80[JPT][hapmap]
rs1809796	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1809797	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1870687	0.80[JPT][hapmap]
rs1908450	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1908451	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1948506	0.80[CEU][hapmap]
rs1975878	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1975879	1.00[JPT][hapmap]
rs1993722	0.80[JPT][hapmap]
rs2056470	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2061570	0.80[JPT][hapmap]
rs2061571	0.80[JPT][hapmap]
rs2061572	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2126112	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2204117	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs2306055	0.80[JPT][hapmap]
rs2391231	0.80[JPT][hapmap]
rs28625259	0.81[AFR][1000 genomes]
rs34021656	0.89[AFR][1000 genomes]
rs34816181	0.87[AFR][1000 genomes]
rs34848208	0.89[ASN][1000 genomes]
rs35239105	0.88[AFR][1000 genomes]
rs3733320	0.80[JPT][hapmap]
rs4383632	0.80[JPT][hapmap];0.82[YRI][hapmap]
rs4385082	0.80[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs4484314	0.89[YRI][hapmap]
rs4493552	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4833395	0.80[JPT][hapmap]
rs4834223	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs4834225	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4834226	0.80[JPT][hapmap]
rs4834229	0.81[JPT][hapmap]
rs4834231	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4975239	0.81[YRI][hapmap]
rs55720227	0.91[AFR][1000 genomes]
rs55849105	0.90[AFR][1000 genomes]
rs62321076	0.89[EUR][1000 genomes]
rs62336165	0.93[AFR][1000 genomes]
rs6534664	0.81[ASN][1000 genomes]
rs6534665	0.82[ASN][1000 genomes]
rs6534668	0.80[JPT][hapmap];0.89[YRI][hapmap]
rs6534669	0.90[CEU][hapmap];0.80[JPT][hapmap];0.89[EUR][1000 genomes]
rs6534670	0.80[JPT][hapmap];0.82[YRI][hapmap]
rs6534672	1.00[CEU][hapmap];0.94[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]
rs6811718	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6815890	0.81[JPT][hapmap];0.80[YRI][hapmap]
rs6818467	0.80[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs6829891	0.80[JPT][hapmap]
rs6839370	0.81[JPT][hapmap]
rs6849546	0.80[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs6849865	0.90[CEU][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes]
rs6850479	0.89[AFR][1000 genomes]
rs6851796	0.80[JPT][hapmap]
rs6856312	0.80[JPT][hapmap];0.84[YRI][hapmap]
rs7661888	0.80[JPT][hapmap]
rs7667562	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7667689	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7671131	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7686130	0.94[CHB][hapmap];1.00[JPT][hapmap];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	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv3390887	chr4:128932563-129207255	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129108200-129149400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:129122800-129149000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:129123000-129144800	Weak transcription	Left Ventricle	heart
4	chr4:129123000-129145800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:129123000-129149000	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:129123000-129149400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:129128200-129149200	Weak transcription	Aorta	Aorta
8	chr4:129128400-129149000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:129129800-129149000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:129130800-129149600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:129133600-129149400	Weak transcription	Pancreas	Pancrea
12	chr4:129134400-129143400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:129134400-129143800	Weak transcription	Fetal Intestine Small	intestine
14	chr4:129134400-129144000	Weak transcription	Fetal Stomach	stomach
15	chr4:129134400-129149200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:129135000-129143800	Weak transcription	Liver	Liver
17	chr4:129135000-129149600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:129141200-129142200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:129141200-129142200	Enhancers	HSMMtube	muscle
20	chr4:129141200-129142400	Enhancers	NHEK	skin
21	chr4:129141200-129143000	Enhancers	Osteobl	bone
22	chr4:129141200-129143200	Enhancers	NHDF-Ad	bronchial
23	chr4:129141400-129142200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr4:129141400-129142400	Enhancers	HSMM	muscle
25	chr4:129141400-129142600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:129141400-129143600	Enhancers	NHLF	lung
27	chr4:129141600-129142200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:129141600-129142200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:129141600-129143200	Enhancers	NH-A	brain
30	chr4:129141800-129142200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:129141800-129142200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:129141800-129142400	Enhancers	HMEC	breast
33	chr4:129141800-129143200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:129141800-129143200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr4:129141800-129143600	Enhancers	Fetal Heart	heart
36	chr4:129142000-129145800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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