Variant report

Variant	rs7678144
Chromosome Location	chr4:55102425-55102426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11133315	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12501810	0.82[AFR][1000 genomes]
rs12505491	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12506290	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12508225	0.81[ASN][1000 genomes]
rs12641563	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12644709	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12644749	0.81[ASN][1000 genomes]
rs1565669	0.81[ASN][1000 genomes]
rs1565670	0.81[ASN][1000 genomes]
rs17084051	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800809	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800810	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800812	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800813	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114039	0.92[GIH][hapmap];0.88[MEX][hapmap]
rs2229307	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2307049	0.82[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs2307050	0.80[JPT][hapmap]
rs28489067	0.80[ASN][1000 genomes]
rs28528897	0.81[ASN][1000 genomes]
rs28600756	0.81[ASN][1000 genomes]
rs4358459	0.81[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs4368668	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4422471	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4608869	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4635872	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864857	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864858	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864859	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864860	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864861	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864864	0.81[ASN][1000 genomes]
rs4864865	0.81[ASN][1000 genomes]
rs56145315	0.81[ASN][1000 genomes]
rs58435984	0.85[ASN][1000 genomes]
rs58727676	0.81[ASN][1000 genomes]
rs60806423	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60863210	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61320297	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554158	0.81[AMR][1000 genomes]
rs6554160	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6554162	0.92[GIH][hapmap];0.92[MEX][hapmap]
rs6554163	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs67279506	0.81[ASN][1000 genomes]
rs67432867	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67600360	0.81[ASN][1000 genomes]
rs6831380	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6832597	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6836215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846502	0.81[AMR][1000 genomes]
rs6850748	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73252942	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73252946	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73252948	0.81[ASN][1000 genomes]
rs7660560	0.82[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs7673027	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673597	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673625	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673853	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673984	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676972	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7677751	0.83[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7679903	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681399	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682912	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7686588	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7688997	0.82[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs7689569	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690503	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691129	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7698425	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890203	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890205	0.81[AMR][1000 genomes]
rs9991165	0.88[AMR][1000 genomes];0.86[ASN][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	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002905	chr4:55093677-55115698	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2763361	chr4:55102425-55107618	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55100600-55104400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:55101000-55103800	Weak transcription	Colonic Mucosa	Colon
3	chr4:55101000-55104200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:55101000-55104400	Weak transcription	HMEC	breast
5	chr4:55101000-55105200	Weak transcription	Aorta	Aorta
6	chr4:55101200-55105800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:55101200-55106400	Weak transcription	Right Atrium	heart
8	chr4:55101400-55102600	Enhancers	Osteobl	bone
9	chr4:55101400-55103000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:55101400-55103200	Weak transcription	Fetal Stomach	stomach
11	chr4:55101400-55104000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:55101400-55104600	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:55101400-55110200	Weak transcription	Fetal Kidney	kidney
14	chr4:55101600-55102600	Transcr. at gene 5' and 3'	NHLF	lung
15	chr4:55101600-55103400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:55102000-55102600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:55102000-55102600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:55102000-55102600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
19	chr4:55102000-55102600	Flanking Active TSS	Ovary	ovary
20	chr4:55102000-55102600	Enhancers	NHDF-Ad	bronchial
21	chr4:55102000-55102800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:55102200-55103000	Weak transcription	Fetal Lung	lung
23	chr4:55102200-55105200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:55102400-55102600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
25	chr4:55102400-55102800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:55102400-55102800	Weak transcription	Placenta	Placenta
27	chr4:55102400-55103400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:55102400-55103800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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