Variant report

Variant	rs984753
Chromosome Location	chr12:45240610-45240611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2703059	1.00[AMR][1000 genomes]
rs61656468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279147	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279183	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs984753	CYP27A1	trans	lymphoblastoid	seeQTL
rs984753	BAMBI	trans	lymphoblastoid	seeQTL
rs984753	SH2D1A	trans	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45220600-45242000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr12:45221800-45242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:45230000-45242200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:45231200-45241600	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr12:45233600-45242000	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr12:45234800-45242000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:45237000-45241400	Enhancers	Primary T cells from cord blood	blood
8	chr12:45237000-45241400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr12:45238400-45242000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:45238400-45242000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:45239800-45241200	Enhancers	Fetal Brain Female	brain
12	chr12:45239800-45241600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr12:45239800-45241800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:45239800-45242000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:45240000-45241000	Enhancers	Fetal Brain Male	brain
16	chr12:45240200-45241000	Enhancers	Duodenum Mucosa	Duodenum
17	chr12:45240200-45241200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:45240200-45241200	Enhancers	Adipose Nuclei	Adipose
19	chr12:45240200-45241400	Enhancers	Dnd41	blood
20	chr12:45240200-45248400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:45240600-45241000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:45240600-45241000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr12:45240600-45241000	Enhancers	Colon Smooth Muscle	Colon
24	chr12:45240600-45242800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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