Variant report

Variant	rs61957424
Chromosome Location	chr13:52506159-52506160
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52505637..52508470-chr13:52586415..52588221,2	MCF-7	breast:
2	chr13:52501775..52503444-chr13:52504796..52507075,2	K562	blood:
3	chr13:52500788..52502899-chr13:52504478..52506226,2	MCF-7	breast:
4	chr13:52502344..52503850-chr13:52505808..52508798,2	MCF-7	breast:
5	chr13:52503688..52506569-chr13:52701656..52704477,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC70-2	chr13:52506091-52506175	NONHSAT033958

No data

Variant related genes	Relation type
ENSG00000253710	Chromatin interaction
ENSG00000197168	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1801247	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282059	0.82[AFR][1000 genomes]
rs60579905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957425	1.00[EUR][1000 genomes]
rs61957447	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957449	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957450	0.83[AFR][1000 genomes]
rs61957453	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957454	0.80[EUR][1000 genomes]
rs61957455	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526807	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526809	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526813	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535794	0.83[EUR][1000 genomes]
rs9535803	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535804	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535805	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535806	0.83[EUR][1000 genomes]
rs9535807	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535808	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535809	0.83[EUR][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	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	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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:64 , 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	chr13:52487000-52507800	Weak transcription	Pancreas	Pancrea
3	chr13:52488000-52507800	Weak transcription	Brain Anterior Caudate	brain
4	chr13:52488000-52508200	Weak transcription	Brain Angular Gyrus	brain
5	chr13:52488000-52508200	Weak transcription	Brain Hippocampus Middle	brain
6	chr13:52488200-52508000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:52489600-52508400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr13:52490000-52509400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr13:52492000-52508400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
12	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr13:52494800-52527000	Weak transcription	Fetal Lung	lung
14	chr13:52495400-52512600	Weak transcription	Colon Smooth Muscle	Colon
15	chr13:52495600-52508200	Weak transcription	Brain Substantia Nigra	brain
16	chr13:52495600-52515000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:52496200-52508200	Weak transcription	Stomach Mucosa	stomach
18	chr13:52496200-52508200	Weak transcription	Spleen	Spleen
19	chr13:52496600-52507200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr13:52496600-52524200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr13:52497400-52508400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:52497600-52507800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr13:52497600-52508000	Weak transcription	Fetal Brain Female	brain
24	chr13:52497600-52508800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr13:52497600-52519600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr13:52499800-52507600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr13:52500200-52508600	Weak transcription	Esophagus	oesophagus
28	chr13:52500400-52508000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr13:52500400-52508600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr13:52500600-52507800	Weak transcription	Gastric	stomach
31	chr13:52500600-52507800	Weak transcription	Lung	lung
32	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr13:52501600-52532400	Strong transcription	HepG2	liver
34	chr13:52502600-52514800	Weak transcription	HSMMtube	muscle
35	chr13:52502800-52506200	Weak transcription	Right Ventricle	heart
36	chr13:52502800-52518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr13:52502800-52529200	Weak transcription	Psoas Muscle	Psoas
38	chr13:52503000-52508000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr13:52504000-52515000	Weak transcription	K562	blood
40	chr13:52504200-52508000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:52504200-52512200	Weak transcription	Fetal Heart	heart
42	chr13:52504200-52533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr13:52504400-52508600	Weak transcription	Colonic Mucosa	Colon
44	chr13:52504400-52509600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr13:52504600-52537000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr13:52505200-52508400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr13:52505600-52520800	Strong transcription	Fetal Intestine Small	intestine
48	chr13:52505600-52531800	Strong transcription	Liver	Liver
49	chr13:52505800-52506600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr13:52505800-52508000	Enhancers	Placenta	Placenta

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