Variant report

Variant	rs7700289
Chromosome Location	chr5:60664356-60664357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10041978	0.86[ASN][1000 genomes]
rs1045352	0.81[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs10939900	0.93[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939901	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939902	0.99[ASN][1000 genomes]
rs10939903	0.86[ASN][1000 genomes]
rs10939905	0.80[ASN][1000 genomes]
rs11742658	0.80[ASN][1000 genomes]
rs11743711	0.88[ASN][1000 genomes]
rs11747564	0.80[ASN][1000 genomes]
rs11749200	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs11750589	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11950318	0.84[ASN][1000 genomes]
rs11952146	0.81[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs11954430	0.82[ASN][1000 genomes]
rs12187112	0.94[ASN][1000 genomes]
rs12188627	0.93[ASN][1000 genomes]
rs12189001	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518479	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520628	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522647	0.86[ASN][1000 genomes]
rs13156100	0.80[ASN][1000 genomes]
rs13157657	0.82[ASN][1000 genomes]
rs13157831	0.80[ASN][1000 genomes]
rs13158675	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13160801	0.82[ASN][1000 genomes]
rs13162358	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163970	0.82[ASN][1000 genomes]
rs13169711	1.00[ASN][1000 genomes]
rs13170135	0.98[ASN][1000 genomes]
rs13170262	0.82[ASN][1000 genomes]
rs13171497	0.80[ASN][1000 genomes]
rs13171757	0.88[ASN][1000 genomes]
rs13172080	0.82[ASN][1000 genomes]
rs13172084	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs13178686	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179091	0.80[ASN][1000 genomes]
rs13181015	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13185068	0.80[ASN][1000 genomes]
rs13186194	0.81[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs13188327	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13188685	0.80[ASN][1000 genomes]
rs1348716	0.82[ASN][1000 genomes]
rs1374043	0.82[ASN][1000 genomes]
rs1445976	0.80[ASN][1000 genomes]
rs1445979	0.86[ASN][1000 genomes]
rs1445980	0.80[ASN][1000 genomes]
rs1445981	0.80[ASN][1000 genomes]
rs1477355	0.86[ASN][1000 genomes]
rs1986252	0.82[ASN][1000 genomes]
rs2034239	0.80[ASN][1000 genomes]
rs2053693	0.80[ASN][1000 genomes]
rs2053694	0.80[ASN][1000 genomes]
rs2276987	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs28610339	0.99[ASN][1000 genomes]
rs34739794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35262187	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4276369	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4392578	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484384	0.83[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604142	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs5027472	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55838118	0.80[ASN][1000 genomes]
rs56035042	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60529601	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60886975	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62368660	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449526	0.81[GIH][hapmap]
rs6449528	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs6449529	1.00[ASN][1000 genomes]
rs6449530	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449531	0.99[ASN][1000 genomes]
rs6449532	0.99[ASN][1000 genomes]
rs6449533	0.99[ASN][1000 genomes]
rs6449535	0.86[ASN][1000 genomes]
rs66775554	0.80[ASN][1000 genomes]
rs6860608	0.93[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6865624	0.80[ASN][1000 genomes]
rs6873712	0.88[JPT][hapmap]
rs6874264	0.80[ASN][1000 genomes]
rs6877610	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878927	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs6879809	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs6881765	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885005	0.99[ASN][1000 genomes]
rs6890351	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs6894675	0.99[ASN][1000 genomes]
rs6895046	0.82[ASN][1000 genomes]
rs7443602	0.80[ASN][1000 genomes]
rs7701440	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7709645	0.99[ASN][1000 genomes]
rs7714457	0.82[ASN][1000 genomes]
rs7714712	0.99[ASN][1000 genomes]
rs7717082	0.82[ASN][1000 genomes]
rs7719647	0.82[ASN][1000 genomes]
rs7722810	0.87[ASN][1000 genomes]
rs7724551	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs7727824	0.99[ASN][1000 genomes]
rs7734879	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv1815974	chr5:60626344-60664356	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60638400-60665200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr5:60640400-60665600	Weak transcription	Gastric	stomach
3	chr5:60641600-60667400	Weak transcription	Fetal Kidney	kidney
4	chr5:60648200-60664600	Weak transcription	Aorta	Aorta
5	chr5:60649000-60666400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:60649400-60664400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:60650000-60664600	Weak transcription	Ovary	ovary
8	chr5:60653400-60667200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:60653600-60666800	Weak transcription	NHEK	skin
10	chr5:60653600-60667400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:60653800-60681200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:60654000-60667400	Weak transcription	Hela-S3	cervix
13	chr5:60654000-60681400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:60654200-60664800	Weak transcription	Brain Germinal Matrix	brain
15	chr5:60654800-60664800	Weak transcription	Primary T cells from cord blood	blood
16	chr5:60656800-60666600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:60657000-60666800	Weak transcription	Small Intestine	intestine
18	chr5:60657200-60664600	Weak transcription	Liver	Liver
19	chr5:60657600-60676400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:60658200-60674400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:60658400-60666800	Weak transcription	Fetal Intestine Small	intestine
22	chr5:60658800-60686600	Weak transcription	Fetal Stomach	stomach
23	chr5:60659000-60664600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:60659000-60664600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:60659000-60665200	Weak transcription	Lung	lung
26	chr5:60659000-60666400	Weak transcription	Left Ventricle	heart
27	chr5:60659000-60666400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:60659000-60666600	Weak transcription	Fetal Intestine Large	intestine
29	chr5:60659000-60667000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:60659000-60674600	Weak transcription	Pancreas	Pancrea
31	chr5:60659000-60681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:60659000-60703800	Weak transcription	Primary B cells from cord blood	blood
33	chr5:60659200-60665200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:60659200-60666400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr5:60659200-60686600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr5:60659400-60664400	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:60659400-60664400	Weak transcription	Fetal Brain Female	brain
38	chr5:60659400-60665200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:60659400-60665600	Weak transcription	HUVEC	blood vessel
40	chr5:60659400-60666400	Weak transcription	A549	lung
41	chr5:60659400-60669400	Weak transcription	NHDF-Ad	bronchial
42	chr5:60659400-60703600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:60659600-60664800	Weak transcription	Adipose Nuclei	Adipose
44	chr5:60659600-60667800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:60659600-60670800	Weak transcription	Fetal Brain Male	brain
46	chr5:60659600-60697600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:60660200-60681600	Weak transcription	HSMM	muscle
48	chr5:60660800-60667400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:60661400-60665200	Enhancers	Brain Substantia Nigra	brain
50	chr5:60661800-60686800	Weak transcription	Monocytes-CD14+_RO01746	blood

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