Variant report

Variant	rs8002488
Chromosome Location	chr13:39261784-39261785
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:39260551..39262193-chr6:28047138..28049723,2	MCF-7	breast:
2	chr13:39259930..39261837-chr13:39400225..39402249,2	MCF-7	breast:
3	chr13:39259553..39261802-chr13:39611603..39613271,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120685	Chromatin interaction
ENSG00000188811	Chromatin interaction
ENSG00000272009	Chromatin interaction
ENSG00000225350	Chromatin interaction
ENSG00000197279	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11147726	0.92[AFR][1000 genomes]
rs11147727	0.92[AFR][1000 genomes]
rs11147728	0.92[AFR][1000 genomes]
rs17058420	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17058423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17058430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17058443	0.99[AFR][1000 genomes]
rs17058452	0.83[AFR][1000 genomes]
rs17058513	0.88[AFR][1000 genomes]
rs41418944	0.82[AFR][1000 genomes]
rs56359648	0.83[AMR][1000 genomes]
rs57001791	0.92[AFR][1000 genomes]
rs59255961	0.91[AFR][1000 genomes]
rs59593155	1.00[AMR][1000 genomes]
rs59939899	0.92[AFR][1000 genomes]
rs60698466	0.85[AFR][1000 genomes]
rs6563630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7336865	0.99[AFR][1000 genomes]
rs7982877	1.00[AMR][1000 genomes]
rs7984183	0.85[AFR][1000 genomes]
rs7984232	0.80[AFR][1000 genomes]
rs7997838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7999409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9671014	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39259600-39261800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr13:39259600-39262000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr13:39259800-39262000	Active TSS	Fetal Kidney	kidney
4	chr13:39260000-39261800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr13:39260000-39261800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:39260000-39261800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr13:39260000-39261800	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr13:39260000-39261800	Active TSS	Aorta	Aorta
9	chr13:39260000-39262000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr13:39260000-39262000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:39260000-39262000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr13:39260000-39262200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr13:39260000-39262200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:39260000-39262200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr13:39260200-39261800	Flanking Active TSS	Liver	Liver
16	chr13:39260200-39261800	Active TSS	Brain Hippocampus Middle	brain
17	chr13:39260200-39262000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:39260200-39262000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr13:39260200-39262000	Active TSS	Fetal Heart	heart
20	chr13:39260200-39262000	Active TSS	Psoas Muscle	Psoas
21	chr13:39260200-39262200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr13:39260200-39262200	Active TSS	Brain Angular Gyrus	brain
23	chr13:39260200-39262200	Active TSS	Brain Substantia Nigra	brain
24	chr13:39260200-39262200	Active TSS	Rectal Smooth Muscle	rectum
25	chr13:39260200-39262200	Active TSS	Right Atrium	heart
26	chr13:39260200-39262400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:39260200-39262400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr13:39260200-39262400	Active TSS	Brain Anterior Caudate	brain
29	chr13:39260200-39262400	Active TSS	Colon Smooth Muscle	Colon
30	chr13:39260400-39261800	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr13:39260400-39261800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
32	chr13:39260400-39261800	Active TSS	Gastric	stomach
33	chr13:39260400-39261800	Active TSS	Left Ventricle	heart
34	chr13:39260400-39262000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
35	chr13:39260400-39262200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr13:39260400-39262200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr13:39260400-39262200	Bivalent/Poised TSS	Fetal Thymus	thymus
38	chr13:39260400-39262400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
39	chr13:39260400-39262400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
40	chr13:39260400-39262600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr13:39260600-39261800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr13:39260600-39262000	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
43	chr13:39260600-39262200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr13:39260600-39262600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
45	chr13:39260600-39262600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
46	chr13:39260600-39263200	Bivalent/Poised TSS	Fetal Lung	lung
47	chr13:39260800-39261800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr13:39260800-39261800	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr13:39260800-39261800	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr13:39260800-39262000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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