Variant report

Variant	rs1858079
Chromosome Location	chr5:127802836-127802837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10035972	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs10040225	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1004965	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10066170	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10068001	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10073062	0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10078570	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10463844	0.89[JPT][hapmap]
rs11241957	0.89[JPT][hapmap]
rs11241959	1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[MKK][hapmap];0.91[YRI][hapmap];0.86[ASN][1000 genomes]
rs13354986	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13361732	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1435514	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1529866	0.92[ASN][1000 genomes]
rs1561007	0.92[ASN][1000 genomes]
rs17164089	0.92[ASN][1000 genomes]
rs17615552	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17677453	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17677603	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1897999	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2043536	1.00[CEU][hapmap]
rs2263510	0.89[JPT][hapmap]
rs2409539	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331067	0.82[YRI][hapmap]
rs331078	0.89[JPT][hapmap]
rs331083	0.89[JPT][hapmap]
rs331087	0.89[JPT][hapmap]
rs34171917	0.95[ASN][1000 genomes]
rs34790038	0.89[ASN][1000 genomes]
rs3805647	0.89[JPT][hapmap]
rs4100587	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4145849	0.89[JPT][hapmap]
rs4385259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4835947	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4835948	0.89[JPT][hapmap]
rs4836373	1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[MKK][hapmap];0.91[YRI][hapmap];0.85[ASN][1000 genomes]
rs4836377	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4836378	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs62390666	0.89[ASN][1000 genomes]
rs62390667	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6595827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6595828	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6595829	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs6595833	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6595835	0.89[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6595838	0.87[ASN][1000 genomes]
rs6859216	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6860114	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6860901	0.85[CHD][hapmap]
rs6864831	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs6865322	0.84[CHD][hapmap]
rs6873438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6882394	0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6892983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6898280	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6898449	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs764368	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7713256	0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7719223	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7721622	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7725788	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7726680	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7726795	0.89[ASN][1000 genomes]
rs7734008	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs892863	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv599698	chr5:127744825-127850855	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
3	nsv1015650	chr5:127745955-127866566	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
4	esv2763497	chr5:127745955-127882468	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv530822	chr5:127777365-127900742	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127772600-127807600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:127773000-127809400	Weak transcription	HMEC	breast
3	chr5:127773400-127830000	Weak transcription	NHEK	skin
4	chr5:127779400-127807400	Weak transcription	Fetal Kidney	kidney
5	chr5:127780400-127806400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:127780800-127805400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:127784000-127826800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:127787400-127806200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:127788800-127810600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:127792200-127807000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:127792200-127808200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:127792400-127812400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:127792800-127805800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:127795800-127806000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:127796200-127812000	Weak transcription	A549	lung
16	chr5:127796400-127826600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:127796800-127807200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:127798400-127807400	Weak transcription	Fetal Intestine Large	intestine
19	chr5:127800400-127845600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:127800600-127804800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:127800600-127804800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:127800600-127807600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr5:127800600-127813400	Weak transcription	Right Ventricle	heart
24	chr5:127800600-127816200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr5:127800800-127804800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:127800800-127806600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:127800800-127827000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr5:127801000-127805400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:127801600-127805600	Weak transcription	Placenta	Placenta
30	chr5:127801800-127803000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:127801800-127803800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr5:127801800-127804000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:127801800-127804000	Enhancers	Fetal Heart	heart
34	chr5:127801800-127805200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:127801800-127805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:127801800-127805800	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:127802200-127803000	Enhancers	Fetal Lung	lung
38	chr5:127802800-127803000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:127802800-127803000	Enhancers	Left Ventricle	heart
40	chr5:127802800-127803000	Enhancers	Ovary	ovary
41	chr5:127802800-127803400	Enhancers	Fetal Stomach	stomach

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