Variant report

Variant	rs11639108
Chromosome Location	chr15:52499645-52499646
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52483314..52485035-chr15:52498952..52501032,2	MCF-7	breast:
2	chr15:52486663..52491950-chr15:52497424..52502756,7	MCF-7	breast:
3	chr15:52498552..52502035-chr15:52503246..52505472,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11070887	0.85[JPT][hapmap]
rs12439660	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441753	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34212289	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35277595	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3751609	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs3794552	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4494485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60705168	0.82[ASN][1000 genomes]
rs7171499	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7183588	0.85[JPT][hapmap]

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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52473200-52513600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52473600-52512400	Weak transcription	Primary B cells from cord blood	blood
3	chr15:52475800-52505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
5	chr15:52484200-52503200	Weak transcription	Lung	lung
6	chr15:52484400-52503800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:52486000-52505800	Weak transcription	Psoas Muscle	Psoas
8	chr15:52487400-52505200	Weak transcription	Thymus	Thymus
9	chr15:52488600-52509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:52488800-52505600	Weak transcription	Fetal Kidney	kidney
11	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:52490400-52503000	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:52495400-52500600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:52495600-52519000	Strong transcription	HepG2	liver
16	chr15:52496000-52500800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:52496000-52505000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:52496200-52500200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:52496200-52501600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:52496200-52505400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:52497200-52505200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:52497400-52499800	Weak transcription	Brain Anterior Caudate	brain
23	chr15:52497400-52501000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr15:52497400-52503000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:52497400-52505000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:52497400-52509400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:52497400-52510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:52497400-52514600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:52497600-52500000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:52497600-52501600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr15:52497600-52502800	Weak transcription	Adipose Nuclei	Adipose
33	chr15:52497600-52503200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr15:52497600-52503200	Weak transcription	Esophagus	oesophagus
35	chr15:52497600-52503200	Weak transcription	Fetal Intestine Small	intestine
36	chr15:52497600-52503200	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:52497600-52503200	Weak transcription	Spleen	Spleen
38	chr15:52497600-52503400	Weak transcription	Fetal Intestine Large	intestine
39	chr15:52497600-52503600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:52497600-52503600	Weak transcription	Primary T cells from cord blood	blood
41	chr15:52497600-52503600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:52497600-52503600	Weak transcription	Colonic Mucosa	Colon
43	chr15:52497600-52504000	Weak transcription	Right Ventricle	heart
44	chr15:52497600-52508800	Weak transcription	Stomach Mucosa	stomach
45	chr15:52497800-52500200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr15:52497800-52500600	Weak transcription	Pancreas	Pancrea
47	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr15:52498000-52500600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr15:52498400-52500800	Enhancers	HUVEC	blood vessel
50	chr15:52498400-52503000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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