Variant report

Variant	rs11853109
Chromosome Location	chr15:73480432-73480433
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73475200..73477819-chr15:73479193..73482817,3	K562	blood:
2	chr15:73478108..73480793-chr15:73480852..73482517,2	MCF-7	breast:
3	chr15:73472565..73474187-chr15:73479031..73481328,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1017809	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1029	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1038136	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11852881	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11856383	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11856433	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11856466	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11857053	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12101540	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12101734	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13329282	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1382780	1.00[CEU][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1648248	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1678245	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16957661	0.85[EUR][1000 genomes]
rs1714529	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1714530	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1714532	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1812363	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1842164	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1895842	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1963253	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1963254	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1979410	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2169952	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2254390	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2254818	1.00[CEU][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619259	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2623990	1.00[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2623994	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2623996	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2624002	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2660823	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680347	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2680348	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680350	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680351	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28547177	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28572029	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28582318	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28676873	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28808999	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28828370	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4238459	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4287530	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4325518	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4539561	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4635304	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4776626	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4777584	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs490567	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs492448	0.87[AMR][1000 genomes]
rs514632	1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs524457	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs533460	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs550212	0.94[YRI][hapmap];0.87[AMR][1000 genomes]
rs55969660	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57453823	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs576414	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6495054	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7176908	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7180017	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73438015	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7403367	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7497831	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8031718	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8034243	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8035717	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8038411	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs899480	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920152	1.00[CEU][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920459	1.00[CEU][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920675	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][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:50 , 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	chr15:73466800-73482000	Weak transcription	Psoas Muscle	Psoas
5	chr15:73468600-73481200	Weak transcription	Lung	lung
6	chr15:73470800-73481600	Weak transcription	Brain Angular Gyrus	brain
7	chr15:73472000-73488400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:73472000-73496800	Weak transcription	Ovary	ovary
9	chr15:73472200-73504600	Weak transcription	Left Ventricle	heart
10	chr15:73473400-73496400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:73474200-73482400	Weak transcription	Gastric	stomach
12	chr15:73474200-73482600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:73474200-73487800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:73474200-73488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:73474200-73498200	Weak transcription	Liver	Liver
16	chr15:73474200-73523800	Weak transcription	Esophagus	oesophagus
17	chr15:73474400-73481800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:73474600-73488000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:73474600-73500600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:73475200-73486800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:73475200-73517600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:73475400-73495600	Weak transcription	Brain Anterior Caudate	brain
23	chr15:73475800-73481200	Weak transcription	Aorta	Aorta
24	chr15:73475800-73492000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:73476000-73480600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:73476000-73482600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:73476000-73487800	Weak transcription	Pancreas	Pancrea
28	chr15:73476000-73492000	Weak transcription	Fetal Intestine Small	intestine
29	chr15:73476000-73493800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:73476000-73494800	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:73476200-73487800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:73476200-73493800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:73476200-73495000	Weak transcription	Brain Substantia Nigra	brain
34	chr15:73476200-73506200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:73476400-73486800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr15:73477200-73492800	Weak transcription	Fetal Stomach	stomach
37	chr15:73477200-73497400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:73477600-73485800	Weak transcription	Fetal Brain Female	brain
39	chr15:73477600-73492000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:73477600-73503800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:73477800-73489000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:73477800-73491400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:73477800-73499200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:73478000-73491800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:73478200-73482000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:73478200-73488600	Weak transcription	Fetal Lung	lung
47	chr15:73478400-73491400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:73478600-73491400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:73479000-73482000	Strong transcription	Fetal Intestine Large	intestine
50	chr15:73480400-73482600	Weak transcription	Fetal Brain Male	brain

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