Variant report

Variant	rs1688879
Chromosome Location	chr12:42505384-42505385
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1226303	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463613	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628871	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1683198	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1683202	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1688854	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1688874	0.81[AMR][1000 genomes]
rs1688884	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1732350	0.80[AMR][1000 genomes]
rs1732351	0.80[AMR][1000 genomes]
rs1994284	0.81[AMR][1000 genomes]
rs3852592	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582378	0.80[AMR][1000 genomes]
rs712106	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs712120	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7303028	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs824697	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs824699	0.80[AMR][1000 genomes]
rs824716	0.80[AMR][1000 genomes]
rs824717	0.81[AMR][1000 genomes]
rs824718	0.81[AMR][1000 genomes]
rs824722	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs824724	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs824726	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs824734	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs824736	0.86[EUR][1000 genomes]
rs824738	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs844046	0.81[AMR][1000 genomes]
rs865420	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42471800-42524400	Weak transcription	Esophagus	oesophagus
2	chr12:42474600-42514400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:42474600-42518800	Weak transcription	Brain Anterior Caudate	brain
4	chr12:42476000-42524400	Weak transcription	Gastric	stomach
5	chr12:42476200-42524400	Weak transcription	Pancreas	Pancrea
6	chr12:42476600-42523800	Weak transcription	Hela-S3	cervix
7	chr12:42478600-42511600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:42479600-42505400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:42480200-42505600	Weak transcription	Fetal Lung	lung
10	chr12:42480200-42512000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:42483600-42511400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:42484400-42524800	Weak transcription	Right Ventricle	heart
13	chr12:42485200-42511600	Weak transcription	NHDF-Ad	bronchial
14	chr12:42485800-42512200	Weak transcription	Brain Angular Gyrus	brain
15	chr12:42486000-42513000	Weak transcription	Aorta	Aorta
16	chr12:42488200-42505400	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:42488400-42512000	Weak transcription	Osteobl	bone
18	chr12:42488600-42518600	Weak transcription	Fetal Brain Male	brain
19	chr12:42488800-42511800	Weak transcription	HepG2	liver
20	chr12:42490800-42506600	Weak transcription	NH-A	brain
21	chr12:42490800-42511200	Weak transcription	HSMM	muscle
22	chr12:42491400-42511200	Weak transcription	A549	lung
23	chr12:42492200-42505400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:42492200-42511400	Weak transcription	Adipose Nuclei	Adipose
25	chr12:42492200-42511600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:42492200-42512400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:42492200-42518600	Weak transcription	K562	blood
28	chr12:42492400-42505400	Weak transcription	GM12878-XiMat	blood
29	chr12:42492400-42511400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:42492400-42511600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:42492400-42511600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:42492400-42512200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:42492400-42512200	Weak transcription	HUVEC	blood vessel
34	chr12:42492600-42511400	Weak transcription	Dnd41	blood
35	chr12:42492600-42511800	Weak transcription	Primary T cells from cord blood	blood
36	chr12:42493000-42505400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:42493000-42511600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:42493000-42511600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr12:42493000-42524400	Weak transcription	Brain Substantia Nigra	brain
40	chr12:42493000-42534400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:42493200-42511400	Weak transcription	HMEC	breast
42	chr12:42493200-42518400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:42493200-42519200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:42497200-42518800	Weak transcription	Psoas Muscle	Psoas
45	chr12:42497600-42505600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:42498400-42505600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:42498800-42505600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr12:42498800-42513000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:42499000-42516800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr12:42499200-42512200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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