Variant report

Variant	rs2496456
Chromosome Location	chr13:38939004-38939005
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:38924316..38926531-chr13:38938318..38940718,2	MCF-7	breast:
2	chr13:38931254..38934078-chr13:38935864..38939575,4	K562	blood:
3	chr13:38936992..38939468-chr13:38949359..38952511,3	K562	blood:
4	chr13:38937794..38939477-chr13:38941816..38944782,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11693	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330958	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330960	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330964	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330965	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360385	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553300	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576610	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576611	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980984	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019520	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150468	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150469	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231323	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231328	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231330	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231332	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481876	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481877	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481879	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481880	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485783	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485785	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485786	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485789	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496473	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496475	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496476	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943581	0.83[ASN][1000 genomes]
rs4943583	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943584	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943585	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943586	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563608	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563609	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326028	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326913	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332974	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7335723	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338958	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285122	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532209	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532218	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548318	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548320	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603368	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986773	1.00[EUR][1000 genomes];1.00[ASN][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	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949406	chr13:38561474-39033484	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv900006	chr13:38924871-38970825	Genic enhancers ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1851668	chr13:38928976-38948851	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38924800-38939400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:38925200-38939600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr13:38925600-38939200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr13:38925800-38939400	Weak transcription	Thymus	Thymus
5	chr13:38925800-38939800	Weak transcription	Small Intestine	intestine
6	chr13:38926000-38939200	Weak transcription	Psoas Muscle	Psoas
7	chr13:38926000-38939400	Weak transcription	Brain Angular Gyrus	brain
8	chr13:38926000-38939800	Weak transcription	Brain Germinal Matrix	brain
9	chr13:38926200-38939200	Weak transcription	Right Ventricle	heart
10	chr13:38926200-38947000	Weak transcription	Ovary	ovary
11	chr13:38926200-38947000	Weak transcription	Hela-S3	cervix
12	chr13:38927400-38943200	Weak transcription	K562	blood
13	chr13:38928600-38939400	Weak transcription	Brain Substantia Nigra	brain
14	chr13:38929400-38939600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr13:38929600-38939400	Weak transcription	Left Ventricle	heart
16	chr13:38929800-38939800	Weak transcription	HSMMtube	muscle
17	chr13:38930600-38939400	Weak transcription	GM12878-XiMat	blood
18	chr13:38931400-38941000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr13:38933600-38939600	Weak transcription	A549	lung
20	chr13:38933600-38940400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr13:38933600-38943000	Weak transcription	Fetal Heart	heart
22	chr13:38933800-38939800	Weak transcription	NHDF-Ad	bronchial
23	chr13:38936000-38939400	Weak transcription	Stomach Mucosa	stomach
24	chr13:38936400-38939400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr13:38936400-38939600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr13:38936400-38939600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr13:38936400-38939600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr13:38936400-38941200	Weak transcription	NHLF	lung
29	chr13:38936400-38947200	Weak transcription	HepG2	liver
30	chr13:38936600-38940200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr13:38937600-38939200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr13:38937600-38939400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr13:38937600-38939400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr13:38937600-38940800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr13:38937600-38941000	Weak transcription	HMEC	breast
36	chr13:38937800-38939600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr13:38937800-38939800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr13:38937800-38940400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr13:38937800-38941000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:38938000-38939200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr13:38938000-38939200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:38938000-38939600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:38938000-38939600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr13:38938000-38939600	Weak transcription	Primary T cells from cord blood	blood
45	chr13:38938000-38939600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr13:38938000-38939600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr13:38938000-38939600	Weak transcription	Colon Smooth Muscle	Colon
48	chr13:38938000-38939600	Weak transcription	Fetal Intestine Large	intestine
49	chr13:38938000-38939600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr13:38938000-38939600	Weak transcription	Fetal Muscle Leg	muscle

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