Variant report

Variant	rs2399476
Chromosome Location	chr3:113005952-113005953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112929939..112931670-chr3:113004277..113006729,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR52-2	chr3:113005777-113007696	NONHSAT091225

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1499898	0.82[ASN][1000 genomes]
rs16845106	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860709	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16860720	0.82[ASN][1000 genomes]
rs16860752	0.83[AFR][1000 genomes]
rs16860770	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860782	0.83[AFR][1000 genomes]
rs17320040	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17320242	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34600669	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271353	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57104308	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59590258	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60070011	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61035513	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9820139	0.86[ASN][1000 genomes]
rs9832953	0.88[ASN][1000 genomes]
rs9849714	0.82[ASN][1000 genomes]
rs9855011	0.82[ASN][1000 genomes]
rs9872998	0.86[ASN][1000 genomes]
rs9878424	0.86[ASN][1000 genomes]
rs998647	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs999365	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
5	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:112995400-113006000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:112995400-113006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
10	chr3:112995400-113035800	Weak transcription	Lung	lung
11	chr3:112995600-113006400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:112995600-113008400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:112995800-113006600	Weak transcription	Fetal Brain Male	brain
14	chr3:112995800-113013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
16	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
17	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:112997000-113006200	Strong transcription	Fetal Intestine Small	intestine
20	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
21	chr3:112997400-113006200	Strong transcription	Fetal Stomach	stomach
22	chr3:112998600-113036000	Weak transcription	Gastric	stomach
23	chr3:113000200-113006000	Weak transcription	HSMMtube	muscle
24	chr3:113000200-113016400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:113000800-113014400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:113001000-113006000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:113001200-113006400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:113001200-113025400	Weak transcription	Brain Anterior Caudate	brain
29	chr3:113001200-113044600	Weak transcription	Fetal Kidney	kidney
30	chr3:113003200-113006200	Strong transcription	Fetal Lung	lung
31	chr3:113003200-113015400	Weak transcription	Brain Germinal Matrix	brain
32	chr3:113003400-113007000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:113003400-113022600	Weak transcription	Colonic Mucosa	Colon
34	chr3:113003800-113006800	Enhancers	HMEC	breast
35	chr3:113003800-113016200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:113003800-113023000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:113004000-113006000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:113004000-113006200	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr3:113004000-113006200	Enhancers	Ovary	ovary
40	chr3:113004000-113006400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:113004000-113007000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:113004000-113007000	Enhancers	NHEK	skin
43	chr3:113004000-113007800	Weak transcription	Fetal Brain Female	brain
44	chr3:113004200-113006000	Weak transcription	Adipose Nuclei	Adipose
45	chr3:113004200-113006000	Weak transcription	Brain Angular Gyrus	brain
46	chr3:113004200-113006800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:113004200-113007200	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr3:113004200-113023800	Weak transcription	Brain Substantia Nigra	brain
49	chr3:113004400-113006000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:113004400-113006200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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