Variant report

Variant	rs56000886
Chromosome Location	chr12:42836309-42836310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1079985	0.87[AFR][1000 genomes]
rs17091121	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17091147	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17091149	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17091151	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17091153	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17091174	0.81[AFR][1000 genomes]
rs17091186	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1982507	0.87[AFR][1000 genomes]
rs55820023	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56315321	0.87[AFR][1000 genomes]
rs56400220	0.81[AFR][1000 genomes]
rs57096261	0.85[AFR][1000 genomes]
rs58065973	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60131568	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60635137	0.87[AFR][1000 genomes]
rs74078013	0.86[AFR][1000 genomes]
rs74078016	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74078022	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74078049	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74078940	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74078951	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74078992	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74079127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74081028	0.87[AFR][1000 genomes]
rs74081065	0.87[AFR][1000 genomes]
rs754011	0.81[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	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42793800-42840400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:42796000-42836400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:42796000-42838000	Weak transcription	HSMMtube	muscle
5	chr12:42816200-42858200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:42816800-42840400	Weak transcription	Fetal Kidney	kidney
7	chr12:42816800-42862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:42817000-42836600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:42817000-42840000	Weak transcription	NHDF-Ad	bronchial
10	chr12:42820000-42858200	Weak transcription	Gastric	stomach
11	chr12:42820200-42853000	Weak transcription	Fetal Heart	heart
12	chr12:42821000-42844000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:42821200-42836600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:42821400-42836600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:42821400-42840200	Weak transcription	HUVEC	blood vessel
16	chr12:42823600-42839600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:42823800-42840600	Weak transcription	NH-A	brain
18	chr12:42826000-42836400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:42826000-42842400	Weak transcription	HSMM	muscle
20	chr12:42826200-42840200	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:42826400-42859000	Weak transcription	Fetal Brain Male	brain
22	chr12:42826600-42858200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:42831000-42836600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
25	chr12:42832800-42845000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:42833000-42836400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:42833200-42836800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr12:42833200-42837200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:42833200-42837400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:42833200-42841000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:42833400-42836400	Weak transcription	Brain Anterior Caudate	brain
32	chr12:42833600-42841400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:42834200-42838200	Strong transcription	Dnd41	blood
34	chr12:42834200-42838800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:42834200-42841200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr12:42834200-42843200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:42834200-42859600	Weak transcription	Brain Substantia Nigra	brain
38	chr12:42834400-42837200	Strong transcription	Primary T cells from cord blood	blood
39	chr12:42834400-42837600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:42834400-42838000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:42834400-42840600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:42834400-42842400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:42834400-42843000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr12:42834400-42843000	Strong transcription	Fetal Thymus	thymus
45	chr12:42834600-42837000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr12:42834600-42837000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr12:42834600-42837000	Strong transcription	Hela-S3	cervix
48	chr12:42834600-42837600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:42834800-42836800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:42834800-42836800	Strong transcription	Primary hematopoietic stem cells	blood

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