Variant report

Variant	rs1479338
Chromosome Location	chr15:73476100-73476101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73475429..73477756-chr15:73487732..73490810,3	MCF-7	breast:
2	chr15:73475200..73477819-chr15:73479193..73482817,3	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1023924	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1038137	0.88[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs10438294	0.82[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10467948	0.88[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11072403	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072406	0.91[ASN][1000 genomes]
rs1116880	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11634084	0.82[EUR][1000 genomes]
rs11634147	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12050658	0.88[EUR][1000 genomes]
rs12050685	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs12050774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902768	0.82[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs13379875	0.94[CHB][hapmap]
rs1479339	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1479340	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1564345	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17762516	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17762600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17829830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17829836	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17829957	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]
rs1812835	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1871385	0.82[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2127277	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2169951	0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2251205	0.82[JPT][hapmap]
rs2415147	0.82[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2415148	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899784	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34013312	0.83[ASN][1000 genomes]
rs35450875	0.87[ASN][1000 genomes]
rs3736510	0.82[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3743489	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs3784793	1.00[CHB][hapmap]
rs3784801	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3985587	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3985588	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4132536	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs4545783	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4777590	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4777598	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs546564	0.81[CEU][hapmap]
rs55646651	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55836604	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55853625	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55868723	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55925663	0.84[ASN][1000 genomes]
rs55939596	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56215298	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56269104	0.84[ASN][1000 genomes]
rs56348595	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56377702	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58060856	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59066156	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62015460	0.92[EUR][1000 genomes]
rs62015484	0.85[EUR][1000 genomes]
rs62015499	0.84[EUR][1000 genomes]
rs62015500	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62015502	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62015504	0.82[EUR][1000 genomes]
rs62016806	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62016809	0.83[ASN][1000 genomes]
rs62016811	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62016814	0.83[ASN][1000 genomes]
rs62016849	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62016851	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62016853	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62016854	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62016856	0.94[EUR][1000 genomes]
rs62016857	0.88[EUR][1000 genomes]
rs62016858	0.93[EUR][1000 genomes]
rs62017774	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62017776	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169083	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7172021	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7172396	0.93[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74022925	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74025262	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs747872	0.82[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs747873	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7497992	0.88[EUR][1000 genomes]
rs8024575	0.91[ASN][1000 genomes]
rs8026121	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs8035925	0.83[ASN][1000 genomes]
rs8042700	0.82[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9806496	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9972347	0.82[EUR][1000 genomes];0.83[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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
2	chr15:73450000-73477400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:73454600-73483000	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:73455200-73500400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:73458600-73478000	Weak transcription	Colonic Mucosa	Colon
6	chr15:73459000-73482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:73466800-73482000	Weak transcription	Psoas Muscle	Psoas
8	chr15:73467800-73476800	Weak transcription	Fetal Brain Male	brain
9	chr15:73468600-73476200	Weak transcription	Small Intestine	intestine
10	chr15:73468600-73481200	Weak transcription	Lung	lung
11	chr15:73470000-73476400	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr15:73470400-73477200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:73470800-73477400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:73470800-73481600	Weak transcription	Brain Angular Gyrus	brain
15	chr15:73471400-73478600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:73472000-73488400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:73472000-73496800	Weak transcription	Ovary	ovary
18	chr15:73472200-73504600	Weak transcription	Left Ventricle	heart
19	chr15:73473400-73496400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:73473800-73476200	Strong transcription	A549	lung
21	chr15:73473800-73476400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:73473800-73477200	Strong transcription	Fetal Stomach	stomach
23	chr15:73474200-73477400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:73474200-73478200	Strong transcription	Fetal Intestine Large	intestine
25	chr15:73474200-73479600	Weak transcription	Fetal Kidney	kidney
26	chr15:73474200-73482400	Weak transcription	Gastric	stomach
27	chr15:73474200-73482600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:73474200-73487800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:73474200-73488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:73474200-73498200	Weak transcription	Liver	Liver
31	chr15:73474200-73523800	Weak transcription	Esophagus	oesophagus
32	chr15:73474400-73477800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr15:73474400-73478000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:73474400-73481800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:73474600-73478200	Strong transcription	Fetal Lung	lung
36	chr15:73474600-73488000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:73474600-73500600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:73474800-73478200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:73475000-73476200	Enhancers	Brain Substantia Nigra	brain
40	chr15:73475000-73476200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr15:73475000-73476400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:73475000-73477200	Strong transcription	Fetal Muscle Leg	muscle
43	chr15:73475000-73477200	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:73475200-73476200	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr15:73475200-73486800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:73475200-73517600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:73475400-73476200	Enhancers	Brain Cingulate Gyrus	brain
48	chr15:73475400-73476200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr15:73475400-73476800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:73475400-73495600	Weak transcription	Brain Anterior Caudate	brain

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