Variant report

Variant	rs3794553
Chromosome Location	chr15:52523850-52523851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52520877..52522858-chr15:52523295..52525074,3	MCF-7	breast:
2	chr15:52521390..52524844-chr15:52525282..52528513,3	MCF-7	breast:
3	chr15:52521161..52523907-chr15:52528053..52529733,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10152377	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10152383	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11070887	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070888	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906784	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2001858	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28730328	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4405492	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6493547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7183588	0.82[EUR][1000 genomes]
rs8042218	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8043150	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv904220	chr15:52485024-52526507	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv1851383	chr15:52501831-52534344	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1537	chr15:52502246-52537067	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
2	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:52501600-52532600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:52501800-52528000	Weak transcription	Fetal Heart	heart
6	chr15:52505400-52526800	Weak transcription	Right Ventricle	heart
7	chr15:52505600-52525600	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:52505600-52549200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:52506400-52548800	Weak transcription	Fetal Kidney	kidney
10	chr15:52509400-52537200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:52509800-52526800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:52510600-52525600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:52512600-52524800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:52512800-52534000	Weak transcription	Colonic Mucosa	Colon
15	chr15:52514000-52539400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:52514400-52525600	Weak transcription	Thymus	Thymus
17	chr15:52514600-52524600	Enhancers	Primary B cells from cord blood	blood
18	chr15:52514600-52524600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:52514800-52524600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:52515000-52524000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr15:52515000-52524000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:52515000-52524800	Enhancers	Primary B cells from peripheral blood	blood
23	chr15:52515600-52524400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:52515600-52525600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr15:52516000-52525600	Weak transcription	Fetal Thymus	thymus
26	chr15:52516000-52549400	Weak transcription	Left Ventricle	heart
27	chr15:52516200-52526400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr15:52516400-52525600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:52516800-52528200	Weak transcription	Spleen	Spleen
30	chr15:52517400-52526800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:52517400-52527000	Weak transcription	Brain Anterior Caudate	brain
32	chr15:52518000-52524600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:52518000-52524800	Weak transcription	Adipose Nuclei	Adipose
34	chr15:52518000-52525800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:52518600-52526800	Weak transcription	Gastric	stomach
36	chr15:52518800-52525600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:52518800-52526200	Weak transcription	Fetal Muscle Leg	muscle
38	chr15:52519000-52524000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:52519000-52524600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:52519000-52525600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr15:52519000-52526200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr15:52519000-52527000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:52519000-52528200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:52520200-52524600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:52520200-52525800	Weak transcription	A549	lung
46	chr15:52520200-52533800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:52521400-52525800	Weak transcription	Esophagus	oesophagus
48	chr15:52521400-52526800	Weak transcription	Liver	Liver
49	chr15:52521600-52524600	Weak transcription	NHEK	skin
50	chr15:52521600-52530400	Weak transcription	Fetal Intestine Large	intestine

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