Variant report

Variant	rs16964770
Chromosome Location	chr15:52501671-52501672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52466781..52469103-chr15:52500146..52502200,2	MCF-7	breast:
2	chr15:52470561..52473090-chr15:52500221..52502576,3	MCF-7	breast:
3	chr15:52500850..52502666-chr15:52514026..52515788,2	MCF-7	breast:
4	chr15:52271043..52273593-chr15:52500641..52502378,2	MCF-7	breast:
5	chr15:52216346..52217850-chr15:52500229..52502926,2	MCF-7	breast:
6	chr15:52473218..52475845-chr15:52500048..52503534,3	MCF-7	breast:
7	chr15:52486663..52491950-chr15:52497424..52502756,7	MCF-7	breast:
8	chr15:52498552..52502035-chr15:52503246..52505472,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259577	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10400852	1.00[EUR][1000 genomes]
rs12443497	1.00[TSI][hapmap]
rs16953085	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs16964735	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16964737	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs16964750	1.00[EUR][1000 genomes]
rs2231296	1.00[EUR][1000 genomes]
rs28656256	1.00[EUR][1000 genomes]
rs28663157	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41494446	1.00[EUR][1000 genomes]
rs59195841	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59289747	1.00[EUR][1000 genomes]
rs60397096	1.00[EUR][1000 genomes]
rs7163133	1.00[EUR][1000 genomes]
rs7164357	1.00[EUR][1000 genomes]
rs7165157	1.00[EUR][1000 genomes]
rs7165527	1.00[EUR][1000 genomes]
rs7165708	1.00[EUR][1000 genomes]
rs7167133	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7171700	1.00[EUR][1000 genomes]
rs7172939	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs7178038	1.00[EUR][1000 genomes]
rs730945	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs73402803	1.00[EUR][1000 genomes]
rs73402824	1.00[EUR][1000 genomes]
rs73402826	1.00[EUR][1000 genomes]
rs73402833	1.00[EUR][1000 genomes]
rs73402839	1.00[EUR][1000 genomes]
rs73402853	1.00[EUR][1000 genomes]
rs73402859	1.00[EUR][1000 genomes]
rs73402869	1.00[EUR][1000 genomes]
rs73402879	1.00[EUR][1000 genomes]
rs73404813	1.00[EUR][1000 genomes]
rs8023921	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8024311	1.00[EUR][1000 genomes]
rs8024767	1.00[EUR][1000 genomes]
rs8035146	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs8040458	1.00[EUR][1000 genomes]
rs8041042	1.00[EUR][1000 genomes]
rs8041128	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8041233	1.00[EUR][1000 genomes]
rs8041355	1.00[EUR][1000 genomes]
rs8041504	1.00[EUR][1000 genomes]

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:70 , 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	chr15:52495600-52519000	Strong transcription	HepG2	liver
15	chr15:52496000-52505000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:52496200-52505400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:52497200-52505200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:52497400-52503000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:52497400-52505000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:52497400-52509400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:52497400-52510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:52497400-52514600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:52497600-52502800	Weak transcription	Adipose Nuclei	Adipose
25	chr15:52497600-52503200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr15:52497600-52503200	Weak transcription	Esophagus	oesophagus
27	chr15:52497600-52503200	Weak transcription	Fetal Intestine Small	intestine
28	chr15:52497600-52503200	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:52497600-52503200	Weak transcription	Spleen	Spleen
30	chr15:52497600-52503400	Weak transcription	Fetal Intestine Large	intestine
31	chr15:52497600-52503600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:52497600-52503600	Weak transcription	Primary T cells from cord blood	blood
33	chr15:52497600-52503600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:52497600-52503600	Weak transcription	Colonic Mucosa	Colon
35	chr15:52497600-52504000	Weak transcription	Right Ventricle	heart
36	chr15:52497600-52508800	Weak transcription	Stomach Mucosa	stomach
37	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr15:52498400-52503000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:52498600-52502000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:52498800-52501800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr15:52499000-52501800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr15:52499000-52502800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:52499000-52503800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:52499000-52504400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:52499000-52505200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:52499000-52515600	Weak transcription	Left Ventricle	heart
47	chr15:52499200-52503000	Weak transcription	Liver	Liver
48	chr15:52499200-52512600	Strong transcription	A549	lung
49	chr15:52499600-52502000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:52500000-52512000	Strong transcription	Rectal Mucosa Donor 29	rectum

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