Variant report

Variant	rs10881106
Chromosome Location	chr12:47807533-47807534
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:47806611-47808201	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47803497..47805265-chr12:47806055..47808260,2	MCF-7	breast:
2	chr12:47803402..47807961-chr12:47809484..47814843,5	K562	blood:

Variant related genes	Relation type
ENSG00000257906	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10748471	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11183872	1.00[YRI][hapmap]
rs1155457	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12814601	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1468195	0.81[CEU][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1919725	0.88[AMR][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	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10881106	C12orf54	cis	parietal	SCAN
rs10881106	SLC38A2	cis	cerebellum	SCAN
rs10881106	RAPGEF3	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47800000-47808800	Enhancers	Fetal Brain Male	brain
2	chr12:47800800-47807600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr12:47801000-47808000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr12:47801200-47808600	Enhancers	Colon Smooth Muscle	Colon
5	chr12:47801400-47807800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr12:47802200-47809000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr12:47802200-47820000	Weak transcription	Aorta	Aorta
8	chr12:47802600-47808000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:47802600-47808000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:47803200-47807600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr12:47803600-47808200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:47804600-47808400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:47804600-47808600	Enhancers	Rectal Smooth Muscle	rectum
14	chr12:47805000-47808600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:47805000-47808600	Enhancers	Primary T cells from cord blood	blood
16	chr12:47805200-47808800	Weak transcription	Brain Anterior Caudate	brain
17	chr12:47805400-47808600	Enhancers	Fetal Intestine Small	intestine
18	chr12:47805600-47807600	Weak transcription	Fetal Brain Female	brain
19	chr12:47806200-47808600	Enhancers	Fetal Intestine Large	intestine
20	chr12:47806200-47809200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:47806600-47808000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:47806600-47809200	Weak transcription	A549	lung
23	chr12:47806800-47807800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:47807000-47808400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr12:47807000-47808600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:47807200-47807600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:47807200-47807600	Enhancers	Duodenum Mucosa	Duodenum

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