Variant report

Variant	rs13173830
Chromosome Location	chr5:112439759-112439760
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10045658	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10058407	0.87[CEU][hapmap]
rs10063834	0.85[EUR][1000 genomes]
rs10067901	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs10074318	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs10223151	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10223152	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10477486	0.91[CEU][hapmap]
rs10478102	0.91[CEU][hapmap]
rs11241190	0.91[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs11743369	0.95[EUR][1000 genomes]
rs11744218	0.95[CEU][hapmap]
rs11744828	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11744956	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11746908	0.95[CEU][hapmap]
rs11750093	0.91[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs12187718	0.89[ASN][1000 genomes]
rs12187866	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12513669	0.84[EUR][1000 genomes]
rs13170088	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13174818	0.82[EUR][1000 genomes]
rs13183472	0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs13190424	0.84[ASN][1000 genomes]
rs2227947	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs28645351	0.85[EUR][1000 genomes]
rs3890775	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs3890776	0.88[EUR][1000 genomes]
rs3922585	0.83[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4283779	0.86[CEU][hapmap]
rs4397121	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs4463174	0.91[CEU][hapmap]
rs4645326	0.95[CEU][hapmap]
rs4705539	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4705546	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4705778	0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4705779	0.88[ASN][1000 genomes]
rs4705782	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6594675	0.81[EUR][1000 genomes]
rs6594679	0.81[EUR][1000 genomes]
rs6594680	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs6861166	0.90[CEU][hapmap]
rs6862481	0.87[CEU][hapmap]
rs6865444	0.81[EUR][1000 genomes]
rs6866566	0.91[CEU][hapmap]
rs6866706	0.87[CEU][hapmap]
rs6869399	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs6873623	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs6874220	0.85[EUR][1000 genomes]
rs6874314	0.85[EUR][1000 genomes]
rs6874595	0.85[EUR][1000 genomes]
rs6879138	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6879633	0.91[CEU][hapmap]
rs6879634	0.84[EUR][1000 genomes]
rs6879942	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs6883605	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6894700	0.81[EUR][1000 genomes]
rs6898297	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs7708475	0.85[EUR][1000 genomes]
rs7713290	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7713336	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7714010	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs7714160	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7714275	0.84[EUR][1000 genomes]
rs7714334	0.84[EUR][1000 genomes]
rs7714349	0.84[EUR][1000 genomes]
rs7714492	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs7714725	0.91[CEU][hapmap]
rs7734411	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs7734511	0.81[EUR][1000 genomes]
rs7736823	0.95[CEU][hapmap]
rs7737329	0.84[EUR][1000 genomes]
rs9326874	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs9326875	0.95[CEU][hapmap];0.84[EUR][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	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112399800-112441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:112411200-112443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:112418400-112441600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:112418600-112441400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:112424400-112448000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:112426000-112441600	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:112426200-112445000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:112426600-112453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:112426800-112450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
12	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
14	chr5:112427000-112440800	Weak transcription	NH-A	brain
15	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
16	chr5:112427200-112448200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:112427600-112441600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:112427600-112442000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:112427600-112443200	Weak transcription	Brain Substantia Nigra	brain
20	chr5:112428000-112440200	Strong transcription	Liver	Liver
21	chr5:112428400-112440200	Strong transcription	Fetal Stomach	stomach
22	chr5:112428600-112445000	Weak transcription	Placenta	Placenta
23	chr5:112430400-112441000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:112431000-112440000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:112431000-112442600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:112431600-112440200	Strong transcription	Ovary	ovary
28	chr5:112432200-112443200	Weak transcription	Lung	lung
29	chr5:112432200-112450200	Weak transcription	Spleen	Spleen
30	chr5:112432200-112454600	Weak transcription	Pancreas	Pancrea
31	chr5:112433600-112439800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:112433600-112441200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:112433800-112443800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr5:112435400-112439800	Strong transcription	Fetal Lung	lung
36	chr5:112435800-112439800	Weak transcription	Right Ventricle	heart
37	chr5:112436000-112442400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:112436400-112440600	Strong transcription	Stomach Smooth Muscle	stomach
39	chr5:112436800-112441400	Strong transcription	NHEK	skin
40	chr5:112437000-112440200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:112437600-112439800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:112437600-112445800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:112437800-112454400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr5:112438000-112439800	Weak transcription	Right Atrium	heart
45	chr5:112438000-112440200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:112438000-112444400	Weak transcription	HMEC	breast
47	chr5:112438000-112450600	Weak transcription	Aorta	Aorta
48	chr5:112438000-112454200	Weak transcription	Psoas Muscle	Psoas
49	chr5:112438200-112439800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:112438200-112444800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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