Variant report

Variant	rs4680360
Chromosome Location	chr3:157094479-157094480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1027603	0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs10936085	0.89[CHB][hapmap]
rs10936086	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936087	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486427	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492874	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492929	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496879	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs12629552	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12636038	0.96[EUR][1000 genomes]
rs12638732	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13087207	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1456097	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1456105	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1456106	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1456108	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs1456110	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1500916	0.89[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1500919	0.86[EUR][1000 genomes]
rs1500920	0.87[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs1545596	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs1546261	0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs1563420	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs1568609	0.91[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs1585080	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1824058	0.95[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1840668	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1840673	0.95[CEU][hapmap];0.88[CHB][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs1869857	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs1869859	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs1965246	0.96[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs2047649	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2085315	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2124497	0.89[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs2168430	0.95[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs2168431	0.89[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs2305620	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2305622	0.96[EUR][1000 genomes]
rs35004310	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3816527	0.90[JPT][hapmap]
rs3816528	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4435581	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4482625	0.83[EUR][1000 genomes]
rs4640512	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4640513	0.80[EUR][1000 genomes]
rs4679793	0.96[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs4680351	0.82[GIH][hapmap]
rs4680358	0.86[EUR][1000 genomes]
rs4680359	0.89[CHB][hapmap]
rs4680367	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs56249701	0.80[EUR][1000 genomes]
rs6441126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441127	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441128	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441129	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6776647	0.82[GIH][hapmap]
rs6801110	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6803628	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs722484	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7614339	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs7617727	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618502	0.83[EUR][1000 genomes]
rs7618737	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7623173	0.95[CEU][hapmap];0.89[CHB][hapmap];0.96[EUR][1000 genomes]
rs7626884	0.90[JPT][hapmap]
rs7629293	0.96[EUR][1000 genomes]
rs7631556	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs7639254	0.91[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9857875	0.95[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs9871290	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878474	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs988587	0.96[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs988588	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs9990136	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4680360	SSR3	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157078200-157102400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:157083600-157105800	Weak transcription	HSMM	muscle
3	chr3:157088000-157108600	Weak transcription	Lung	lung
4	chr3:157088600-157105400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:157090200-157096800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:157091200-157095200	Enhancers	NHDF-Ad	bronchial
7	chr3:157091400-157095000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:157091400-157095000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:157091400-157096000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:157091600-157095000	Enhancers	NHLF	lung
11	chr3:157091600-157097200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:157091800-157108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:157091800-157142600	Weak transcription	Pancreas	Pancrea
14	chr3:157092000-157096000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:157092800-157095000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:157092800-157095000	Enhancers	HUVEC	blood vessel
17	chr3:157093200-157094600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:157093200-157094800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:157093200-157095200	Enhancers	Osteobl	bone
20	chr3:157093600-157095000	Enhancers	Fetal Brain Male	brain
21	chr3:157093600-157095000	Enhancers	Fetal Lung	lung
22	chr3:157093600-157095200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:157093800-157094600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:157093800-157095200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:157093800-157095400	Enhancers	Fetal Stomach	stomach
26	chr3:157094000-157094600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr3:157094000-157094800	Enhancers	Brain Germinal Matrix	brain
28	chr3:157094000-157094800	Enhancers	Fetal Brain Female	brain
29	chr3:157094000-157095000	Enhancers	Brain Hippocampus Middle	brain
30	chr3:157094200-157106000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:157094200-157106000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:157094200-157106200	Weak transcription	NH-A	brain

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