Variant report

Variant	rs17677555
Chromosome Location	chr5:127852612-127852613
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1000488	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11738659	0.80[ASN][1000 genomes]
rs11741832	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11742635	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs13155917	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13159256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13163820	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13164781	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13175872	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs13177608	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13177978	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13180029	1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs13180243	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13181926	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13182859	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13184921	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1561004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17677069	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs17677346	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017775	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs331068	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs34250874	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34628042	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34722489	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34797235	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34952159	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35776217	0.84[ASN][1000 genomes]
rs3805646	0.89[JPT][hapmap]
rs3805651	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3805653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3828661	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4836375	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[ASN][1000 genomes]
rs62390664	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62390668	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62390670	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62391614	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391642	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391643	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66968874	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72785142	0.90[AFR][1000 genomes];0.96[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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127824800-127853800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:127826200-127859800	Weak transcription	NH-A	brain
3	chr5:127827200-127870400	Weak transcription	Fetal Kidney	kidney
4	chr5:127827600-127854000	Weak transcription	HUVEC	blood vessel
5	chr5:127840200-127853600	Weak transcription	HMEC	breast
6	chr5:127840200-127854200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:127840200-127859600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:127840200-127870400	Weak transcription	Left Ventricle	heart
9	chr5:127840200-127872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:127840400-127853600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:127840400-127853600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:127840400-127864200	Weak transcription	Fetal Intestine Large	intestine
13	chr5:127840400-127867600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:127840800-127853000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:127841000-127853600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:127841000-127853800	Weak transcription	Fetal Stomach	stomach
17	chr5:127841000-127859600	Weak transcription	NHEK	skin
18	chr5:127841000-127870200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:127841200-127853800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:127841400-127853800	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:127842600-127863600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:127843400-127857800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr5:127843600-127853000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr5:127844200-127860000	Weak transcription	Fetal Lung	lung
25	chr5:127844400-127855800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:127845600-127853600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:127845600-127867800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:127845600-127870400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:127846000-127867800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:127846200-127853600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:127846200-127853600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:127847400-127853800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:127847400-127862200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:127847400-127869000	Weak transcription	NHDF-Ad	bronchial
35	chr5:127848400-127853800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:127851200-127853400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:127851200-127853600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr5:127851400-127853800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:127851400-127856400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:127851600-127853200	Weak transcription	Placenta	Placenta
41	chr5:127851600-127853600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:127851800-127853600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:127852200-127853600	Weak transcription	Fetal Heart	heart
44	chr5:127852400-127860000	Weak transcription	A549	lung
45	chr5:127852600-127853400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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