Variant report

Variant	rs12498836
Chromosome Location	chr4:56860884-56860885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12506140	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12512313	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13129724	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13135276	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34065759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34558195	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35032869	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35282347	0.85[AMR][1000 genomes]
rs35869805	0.84[AMR][1000 genomes]
rs35921148	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4864566	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4865044	0.85[AMR][1000 genomes]
rs4865047	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56209204	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6856844	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601608	0.85[AMR][1000 genomes]
rs71601613	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9312669	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56815800-56875000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:56816200-56873400	Weak transcription	Pancreas	Pancrea
3	chr4:56816200-56884200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:56816200-56887800	Weak transcription	Gastric	stomach
5	chr4:56816400-56866000	Weak transcription	Spleen	Spleen
6	chr4:56816400-56890800	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:56816600-56865800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:56816600-56890600	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:56816600-56896400	Weak transcription	Fetal Heart	heart
10	chr4:56816800-56865800	Weak transcription	Small Intestine	intestine
11	chr4:56816800-56869800	Weak transcription	HepG2	liver
12	chr4:56817400-56885400	Weak transcription	NHDF-Ad	bronchial
13	chr4:56819000-56897400	Weak transcription	HSMMtube	muscle
14	chr4:56819200-56890600	Weak transcription	NHLF	lung
15	chr4:56820600-56892400	Weak transcription	Hela-S3	cervix
16	chr4:56822200-56873600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:56822400-56865800	Weak transcription	Psoas Muscle	Psoas
18	chr4:56823600-56893800	Weak transcription	HMEC	breast
19	chr4:56825200-56865800	Weak transcription	Aorta	Aorta
20	chr4:56825600-56870000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:56828200-56884200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:56829200-56881400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:56829400-56865600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:56829600-56890600	Weak transcription	A549	lung
25	chr4:56832400-56865800	Weak transcription	Liver	Liver
26	chr4:56833000-56877200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:56835400-56904800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:56837200-56905000	Weak transcription	Brain Substantia Nigra	brain
29	chr4:56838200-56865400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:56839800-56896600	Weak transcription	Brain Angular Gyrus	brain
31	chr4:56840000-56865800	Weak transcription	Esophagus	oesophagus
32	chr4:56840200-56865800	Weak transcription	Fetal Brain Female	brain
33	chr4:56840200-56878000	Weak transcription	NHEK	skin
34	chr4:56840200-56884600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:56840600-56866600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:56842800-56890800	Weak transcription	Osteobl	bone
37	chr4:56844200-56891000	Weak transcription	Colonic Mucosa	Colon
38	chr4:56847000-56873800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr4:56847200-56891000	Weak transcription	Right Ventricle	heart
40	chr4:56847400-56864400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:56847600-56866400	Weak transcription	Placenta	Placenta
42	chr4:56848400-56865400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:56848400-56865600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr4:56848400-56865600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:56848400-56865600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:56848600-56865600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:56848800-56864200	Weak transcription	NH-A	brain
48	chr4:56848800-56878000	Weak transcription	HSMM	muscle
49	chr4:56850400-56868400	Weak transcription	Fetal Brain Male	brain
50	chr4:56850800-56872200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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