Variant report

Variant	rs3985588
Chromosome Location	chr15:73482002-73482003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73475200..73477819-chr15:73479193..73482817,3	K562	blood:
2	chr15:73478108..73480793-chr15:73480852..73482517,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1023924	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1038137	0.87[ASN][1000 genomes]
rs10467948	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11072403	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11072406	0.92[ASN][1000 genomes]
rs1116880	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11634147	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12050658	0.93[EUR][1000 genomes]
rs12050685	0.93[EUR][1000 genomes]
rs12050774	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12902768	0.91[ASN][1000 genomes]
rs1479338	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1479339	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479340	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1564345	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17762516	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17762600	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17829830	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17829836	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17829957	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1812835	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1871385	0.89[ASN][1000 genomes]
rs2127277	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2169951	0.84[ASN][1000 genomes]
rs2415147	0.88[ASN][1000 genomes]
rs2415148	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899784	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34013312	0.83[ASN][1000 genomes]
rs35450875	0.88[ASN][1000 genomes]
rs3736510	0.88[ASN][1000 genomes]
rs3784801	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3985587	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4545783	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4777590	0.82[ASN][1000 genomes]
rs4777598	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55646651	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55836604	0.84[ASN][1000 genomes]
rs55853625	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55868723	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55925663	0.85[ASN][1000 genomes]
rs55939596	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56215298	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56269104	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56348595	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56377702	0.84[ASN][1000 genomes]
rs58060856	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59066156	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62015460	0.86[EUR][1000 genomes]
rs62015500	0.91[AMR][1000 genomes]
rs62015502	0.89[AMR][1000 genomes]
rs62016806	0.84[ASN][1000 genomes]
rs62016809	0.84[ASN][1000 genomes]
rs62016811	0.82[ASN][1000 genomes]
rs62016814	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62016849	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62016851	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62016853	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62016854	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62016856	0.87[EUR][1000 genomes]
rs62016857	0.93[EUR][1000 genomes]
rs62016858	0.87[EUR][1000 genomes]
rs62017774	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62017776	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7169083	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7172021	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7172396	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74022925	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74025262	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747872	0.89[ASN][1000 genomes]
rs747873	0.89[ASN][1000 genomes]
rs7497992	0.93[EUR][1000 genomes]
rs8024575	0.92[ASN][1000 genomes]
rs8026121	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8035925	0.83[ASN][1000 genomes]
rs8042700	0.92[ASN][1000 genomes]
rs9806496	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9972347	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	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
8	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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73454600-73483000	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:73455200-73500400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:73459000-73482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:73472000-73488400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:73472000-73496800	Weak transcription	Ovary	ovary
6	chr15:73472200-73504600	Weak transcription	Left Ventricle	heart
7	chr15:73473400-73496400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:73474200-73482400	Weak transcription	Gastric	stomach
9	chr15:73474200-73482600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:73474200-73487800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:73474200-73488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:73474200-73498200	Weak transcription	Liver	Liver
13	chr15:73474200-73523800	Weak transcription	Esophagus	oesophagus
14	chr15:73474600-73488000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:73474600-73500600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:73475200-73486800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:73475200-73517600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:73475400-73495600	Weak transcription	Brain Anterior Caudate	brain
19	chr15:73475800-73492000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:73476000-73482600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:73476000-73487800	Weak transcription	Pancreas	Pancrea
22	chr15:73476000-73492000	Weak transcription	Fetal Intestine Small	intestine
23	chr15:73476000-73493800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:73476000-73494800	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:73476200-73487800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr15:73476200-73493800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:73476200-73495000	Weak transcription	Brain Substantia Nigra	brain
28	chr15:73476200-73506200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:73476400-73486800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:73477200-73492800	Weak transcription	Fetal Stomach	stomach
31	chr15:73477200-73497400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:73477600-73485800	Weak transcription	Fetal Brain Female	brain
33	chr15:73477600-73492000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:73477600-73503800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:73477800-73489000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:73477800-73491400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:73477800-73499200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:73478000-73491800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:73478200-73488600	Weak transcription	Fetal Lung	lung
40	chr15:73478400-73491400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:73478600-73491400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:73480400-73482600	Weak transcription	Fetal Brain Male	brain
43	chr15:73481800-73482200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:73481800-73482600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:73482000-73483200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:73482000-73492600	Weak transcription	Fetal Intestine Large	intestine
47	chr15:73482000-73504600	Weak transcription	Aorta	Aorta

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