Variant report

Variant	rs10939902
Chromosome Location	chr5:60727990-60727991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10041978	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1045352	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs10939900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10939901	0.99[ASN][1000 genomes]
rs10939903	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11743711	0.89[ASN][1000 genomes]
rs11749200	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs11750589	0.98[ASN][1000 genomes]
rs11950318	0.86[ASN][1000 genomes]
rs11952146	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs11954430	0.81[ASN][1000 genomes]
rs11954859	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12187112	0.95[ASN][1000 genomes]
rs12188627	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12189001	0.99[ASN][1000 genomes]
rs12518479	0.99[ASN][1000 genomes]
rs12520628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12522647	0.87[ASN][1000 genomes]
rs12523278	0.88[YRI][hapmap]
rs13157657	0.81[ASN][1000 genomes]
rs13158675	0.99[ASN][1000 genomes]
rs13160801	0.81[ASN][1000 genomes]
rs13162358	0.99[ASN][1000 genomes]
rs13163970	0.81[ASN][1000 genomes]
rs13169711	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13170135	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13170262	0.81[ASN][1000 genomes]
rs13171757	0.89[ASN][1000 genomes]
rs13172080	0.81[ASN][1000 genomes]
rs13172084	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs13178686	0.99[ASN][1000 genomes]
rs13181015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13186194	0.80[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs13188327	0.92[ASN][1000 genomes]
rs1348716	0.81[ASN][1000 genomes]
rs1374043	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1445976	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1445979	0.87[ASN][1000 genomes]
rs1477355	0.87[ASN][1000 genomes]
rs1986252	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2053694	0.80[AMR][1000 genomes]
rs2276987	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs28610339	1.00[ASN][1000 genomes]
rs34739794	0.96[ASN][1000 genomes]
rs35262187	0.99[ASN][1000 genomes]
rs4276369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4392578	0.99[ASN][1000 genomes]
rs4484384	0.99[ASN][1000 genomes]
rs4604142	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700418	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5027472	0.90[ASN][1000 genomes]
rs56035042	0.99[ASN][1000 genomes]
rs60529601	0.99[ASN][1000 genomes]
rs60886975	0.99[ASN][1000 genomes]
rs62368660	0.99[ASN][1000 genomes]
rs6449528	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449529	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6449531	1.00[ASN][1000 genomes]
rs6449532	1.00[ASN][1000 genomes]
rs6449533	1.00[ASN][1000 genomes]
rs6449535	0.87[ASN][1000 genomes]
rs6860608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6873712	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6877610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6878927	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6879809	0.85[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6881765	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6885005	1.00[ASN][1000 genomes]
rs6890351	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6894675	1.00[ASN][1000 genomes]
rs6895046	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6898746	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7700289	0.99[ASN][1000 genomes]
rs7701440	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7709645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714457	0.81[ASN][1000 genomes]
rs7714712	1.00[ASN][1000 genomes]
rs7717082	0.81[ASN][1000 genomes]
rs7719647	0.81[ASN][1000 genomes]
rs7720894	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7722810	0.88[ASN][1000 genomes]
rs7724551	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7727824	1.00[ASN][1000 genomes]
rs7732234	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7734879	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60706000-60728000	Weak transcription	Fetal Intestine Small	intestine
2	chr5:60711000-60735800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr5:60713400-60732800	Weak transcription	Small Intestine	intestine
4	chr5:60719200-60729400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr5:60719800-60745200	Weak transcription	NHDF-Ad	bronchial
6	chr5:60720000-60733800	Weak transcription	NHLF	lung
7	chr5:60720000-60736400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:60720000-60737400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:60720400-60728200	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:60720400-60734000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:60720600-60743200	Weak transcription	HSMMtube	muscle
12	chr5:60721000-60733000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:60721600-60728000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:60721800-60728200	Weak transcription	Right Ventricle	heart
15	chr5:60725600-60728000	Enhancers	Brain Substantia Nigra	brain
16	chr5:60725600-60728000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:60725600-60732600	Weak transcription	Fetal Heart	heart
18	chr5:60725600-60737400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr5:60725800-60728000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:60725800-60728000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:60725800-60732800	Weak transcription	Esophagus	oesophagus
22	chr5:60725800-60732800	Weak transcription	Pancreas	Pancrea
23	chr5:60726000-60728000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:60726000-60728000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:60726000-60728000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:60726000-60728000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:60726000-60729200	Weak transcription	Gastric	stomach
28	chr5:60726000-60730800	Weak transcription	Fetal Brain Female	brain
29	chr5:60726000-60732800	Weak transcription	Left Ventricle	heart
30	chr5:60726000-60732800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:60726000-60733800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:60726000-60736600	Weak transcription	Right Atrium	heart
33	chr5:60726600-60728000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:60726800-60728000	Weak transcription	Brain Angular Gyrus	brain
35	chr5:60726800-60728000	Weak transcription	Brain Anterior Caudate	brain
36	chr5:60726800-60728000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:60726800-60745600	Weak transcription	Stomach Mucosa	stomach
38	chr5:60727000-60732000	Weak transcription	Liver	Liver
39	chr5:60727200-60728600	Enhancers	Fetal Stomach	stomach
40	chr5:60727200-60729000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr5:60727400-60728000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:60727600-60728000	Enhancers	Brain Cingulate Gyrus	brain
43	chr5:60727600-60728400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:60727600-60728400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:60727600-60728400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:60727600-60728600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr5:60727600-60728600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr5:60727600-60728600	Enhancers	HMEC	breast
49	chr5:60727600-60728800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:60727800-60728000	Active TSS	Brain Hippocampus Middle	brain

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