Variant report

Variant	rs17829957
Chromosome Location	chr15:73485897-73485898
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1023924	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1038137	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10438294	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10467948	0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs11072403	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11072406	0.92[ASN][1000 genomes]
rs1116880	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11634084	0.82[EUR][1000 genomes]
rs11634147	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12050658	0.87[EUR][1000 genomes]
rs12050685	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs12050774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050848	0.82[JPT][hapmap]
rs12708506	0.82[JPT][hapmap]
rs12902768	0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs12907139	0.80[JPT][hapmap]
rs13379875	0.94[CHB][hapmap]
rs1479338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1479339	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479340	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1564345	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17762516	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17762600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17829830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17829836	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1812835	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1871385	0.88[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs2127277	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2169951	0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2251205	0.82[JPT][hapmap]
rs2415147	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2415148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899784	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34013312	0.83[ASN][1000 genomes]
rs35450875	0.88[ASN][1000 genomes]
rs3736510	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3743489	0.87[CHB][hapmap]
rs3784793	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs3784801	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3985587	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3985588	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132536	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs4375637	0.80[CHB][hapmap]
rs4545783	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4777590	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4777598	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs546564	0.92[CEU][hapmap]
rs55646651	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55836604	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55853625	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55868723	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55925663	0.85[ASN][1000 genomes]
rs55939596	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56215298	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56269104	0.84[ASN][1000 genomes]
rs56348595	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56377702	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58060856	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59066156	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62015460	0.92[EUR][1000 genomes]
rs62015484	0.84[EUR][1000 genomes]
rs62015499	0.84[EUR][1000 genomes]
rs62015500	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62015502	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62015504	0.82[EUR][1000 genomes]
rs62016806	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62016809	0.84[ASN][1000 genomes]
rs62016811	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62016814	0.84[ASN][1000 genomes]
rs62016849	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62016851	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62016853	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62016854	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62016856	0.93[EUR][1000 genomes]
rs62016857	0.87[EUR][1000 genomes]
rs62016858	0.92[EUR][1000 genomes]
rs62017774	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62017776	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7169083	0.85[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7172021	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7172396	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74022925	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74025262	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747872	0.88[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs747873	0.87[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs7497992	0.87[EUR][1000 genomes]
rs8024575	0.92[ASN][1000 genomes]
rs8026121	0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs8035925	0.83[ASN][1000 genomes]
rs8042700	0.82[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9806496	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9972347	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73455200-73500400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:73472000-73488400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:73472000-73496800	Weak transcription	Ovary	ovary
4	chr15:73472200-73504600	Weak transcription	Left Ventricle	heart
5	chr15:73473400-73496400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:73474200-73487800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:73474200-73488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:73474200-73498200	Weak transcription	Liver	Liver
9	chr15:73474200-73523800	Weak transcription	Esophagus	oesophagus
10	chr15:73474600-73488000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:73474600-73500600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:73475200-73486800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:73475200-73517600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:73475400-73495600	Weak transcription	Brain Anterior Caudate	brain
15	chr15:73475800-73492000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:73476000-73487800	Weak transcription	Pancreas	Pancrea
17	chr15:73476000-73492000	Weak transcription	Fetal Intestine Small	intestine
18	chr15:73476000-73493800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr15:73476000-73494800	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:73476200-73487800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:73476200-73493800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:73476200-73495000	Weak transcription	Brain Substantia Nigra	brain
23	chr15:73476200-73506200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:73476400-73486800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:73477200-73492800	Weak transcription	Fetal Stomach	stomach
26	chr15:73477200-73497400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:73477600-73492000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:73477600-73503800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:73477800-73489000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:73477800-73491400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:73477800-73499200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:73478000-73491800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:73478200-73488600	Weak transcription	Fetal Lung	lung
34	chr15:73478400-73491400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:73478600-73491400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:73482000-73492600	Weak transcription	Fetal Intestine Large	intestine
37	chr15:73482000-73504600	Weak transcription	Aorta	Aorta
38	chr15:73483000-73486000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:73483000-73487400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:73483000-73493800	Weak transcription	Adipose Nuclei	Adipose
41	chr15:73483400-73489000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:73483600-73505800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:73483800-73494800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:73485800-73486800	Enhancers	Fetal Brain Female	brain
45	chr15:73485800-73487400	Enhancers	Fetal Brain Male	brain
46	chr15:73485800-73488800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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