Variant report

Variant	rs1897999
Chromosome Location	chr5:127861612-127861613
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10035972	0.92[ASN][1000 genomes]
rs10040225	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1004965	0.93[ASN][1000 genomes]
rs10066170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068001	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10073062	0.92[ASN][1000 genomes]
rs10078570	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11241959	0.81[ASN][1000 genomes]
rs13354986	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13361732	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1435514	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1529866	0.94[ASN][1000 genomes]
rs1561007	0.94[ASN][1000 genomes]
rs17164089	0.94[ASN][1000 genomes]
rs17615552	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17677453	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17677603	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1858079	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2409539	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34171917	0.87[ASN][1000 genomes]
rs34790038	0.97[ASN][1000 genomes]
rs4100587	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4385259	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835947	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4835948	0.81[AFR][1000 genomes]
rs4836377	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4836378	0.94[ASN][1000 genomes]
rs62390666	0.97[ASN][1000 genomes]
rs62390667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595827	0.89[ASN][1000 genomes]
rs6595828	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6595829	0.94[ASN][1000 genomes]
rs6595833	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6595835	0.97[ASN][1000 genomes]
rs6595838	0.95[ASN][1000 genomes]
rs6859216	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6860114	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6864831	0.94[ASN][1000 genomes]
rs6873438	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6882394	0.92[ASN][1000 genomes]
rs6892983	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6898280	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6898449	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs764368	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7713256	0.87[ASN][1000 genomes]
rs7719223	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7721622	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7725788	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7726680	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7726795	0.97[ASN][1000 genomes]
rs7734008	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs892863	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	nsv427734	chr5:127805281-128088632	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1019560	chr5:127814656-127873680	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv537895	chr5:127814656-127873680	ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127827200-127870400	Weak transcription	Fetal Kidney	kidney
2	chr5:127840200-127870400	Weak transcription	Left Ventricle	heart
3	chr5:127840200-127872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:127840400-127864200	Weak transcription	Fetal Intestine Large	intestine
5	chr5:127840400-127867600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:127841000-127870200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:127842600-127863600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:127845600-127867800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:127845600-127870400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:127846000-127867800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:127847400-127862200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:127847400-127869000	Weak transcription	NHDF-Ad	bronchial
13	chr5:127852800-127867800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:127853200-127872400	Weak transcription	Osteobl	bone
15	chr5:127853400-127864800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:127853400-127867600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:127853600-127867800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:127853800-127862800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:127854000-127872000	Weak transcription	Ovary	ovary
20	chr5:127855000-127862000	Weak transcription	HUVEC	blood vessel
21	chr5:127855000-127863600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:127855000-127867600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:127855000-127871200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:127855400-127867800	Weak transcription	Fetal Stomach	stomach
25	chr5:127856000-127862400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:127857800-127869200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:127858200-127861800	Weak transcription	HMEC	breast
28	chr5:127858200-127862000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:127858600-127863200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:127858600-127864600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr5:127859200-127863200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:127859400-127866600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:127859600-127864200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:127859800-127861800	Strong transcription	NH-A	brain
35	chr5:127860000-127864200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr5:127860000-127868400	Genic enhancers	Fetal Heart	heart
37	chr5:127860200-127870400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:127860400-127864800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:127860800-127864000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr5:127861000-127862600	Weak transcription	Placenta	Placenta
41	chr5:127861000-127870600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:127861000-127871000	Weak transcription	A549	lung
43	chr5:127861000-127871800	Weak transcription	Fetal Lung	lung
44	chr5:127861200-127862000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr5:127861400-127861800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:127861400-127862800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:127861400-127864000	Weak transcription	NHEK	skin
48	chr5:127861400-127867800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:127861600-127863600	Weak transcription	Fetal Muscle Leg	muscle

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