Variant report

Variant	rs61957425
Chromosome Location	chr13:52510346-52510347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52509889..52510481-chr13:52701521..52702501,2	MCF-7	breast:
2	chr13:52509585..52510535-chr13:52701601..52702261,3	K562	blood:
3	chr13:52509591..52510539-chr13:52701676..52702543,4	MCF-7	breast:
4	chr13:52485914..52486609-chr13:52509619..52510504,2	MCF-7	breast:
5	chr13:52508686..52511776-chr13:52512431..52515057,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197168	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1801247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60579905	1.00[EUR][1000 genomes]
rs61957235	1.00[AFR][1000 genomes]
rs61957424	1.00[EUR][1000 genomes]
rs61957447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61957449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61957453	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61957454	0.80[EUR][1000 genomes]
rs61957455	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8002753	1.00[EUR][1000 genomes]
rs9526807	1.00[EUR][1000 genomes]
rs9526809	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9526813	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535794	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535804	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9535805	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9535806	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535808	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9535809	0.83[EUR][1000 genomes]
rs9535827	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv455888	chr13:52491193-52570728	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv561649	chr13:52491193-52570728	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52486400-52523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
4	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr13:52494800-52527000	Weak transcription	Fetal Lung	lung
6	chr13:52495400-52512600	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:52495600-52515000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:52496600-52524200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:52497600-52519600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:52501600-52532400	Strong transcription	HepG2	liver
12	chr13:52502600-52514800	Weak transcription	HSMMtube	muscle
13	chr13:52502800-52518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr13:52502800-52529200	Weak transcription	Psoas Muscle	Psoas
15	chr13:52504000-52515000	Weak transcription	K562	blood
16	chr13:52504200-52512200	Weak transcription	Fetal Heart	heart
17	chr13:52504200-52533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr13:52504600-52537000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr13:52505600-52520800	Strong transcription	Fetal Intestine Small	intestine
20	chr13:52505600-52531800	Strong transcription	Liver	Liver
21	chr13:52505800-52513600	Strong transcription	Brain Germinal Matrix	brain
22	chr13:52505800-52513800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr13:52505800-52514000	Strong transcription	Fetal Stomach	stomach
24	chr13:52505800-52527200	Strong transcription	Fetal Intestine Large	intestine
25	chr13:52506000-52510600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:52506000-52513400	Strong transcription	Left Ventricle	heart
27	chr13:52506000-52513400	Strong transcription	Ovary	ovary
28	chr13:52506000-52517200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr13:52506000-52520800	Strong transcription	Adipose Nuclei	Adipose
30	chr13:52506000-52527200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr13:52506800-52524400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr13:52507000-52517200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr13:52507200-52513400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr13:52507400-52517400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:52507400-52518400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:52507800-52513400	Strong transcription	Pancreas	Pancrea
37	chr13:52508000-52511400	Weak transcription	Placenta	Placenta
38	chr13:52508000-52512800	Strong transcription	Fetal Brain Female	brain
39	chr13:52508000-52514000	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr13:52508000-52532200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr13:52508200-52513400	Strong transcription	Brain Hippocampus Middle	brain
42	chr13:52508400-52513200	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr13:52508600-52511000	Strong transcription	Colonic Mucosa	Colon
44	chr13:52508800-52511200	Weak transcription	Stomach Mucosa	stomach
45	chr13:52509000-52518200	Weak transcription	Esophagus	oesophagus
46	chr13:52509000-52530000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr13:52509200-52510800	Weak transcription	Lung	lung
48	chr13:52509200-52511200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr13:52509200-52511400	Weak transcription	Brain Angular Gyrus	brain
50	chr13:52509200-52511600	Weak transcription	Rectal Mucosa Donor 31	rectum

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