Variant report

Variant	rs12412106
Chromosome Location	chr10:90734906-90734907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11812622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11819114	0.86[CEU][hapmap]
rs17447091	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2862834	1.00[CHB][hapmap]
rs3758483	1.00[CHB][hapmap]
rs61852571	0.83[AMR][1000 genomes]
rs72809340	1.00[AFR][1000 genomes]
rs730755	1.00[JPT][hapmap];1.00[AFR][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	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12412106	IFIT2	cis	parietal	SCAN
rs12412106	LYPD3	trans	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90724800-90739000	Weak transcription	Small Intestine	intestine
2	chr10:90733800-90735400	Active TSS	Aorta	Aorta
3	chr10:90734200-90735400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:90734400-90735000	Active TSS	NHLF	lung
5	chr10:90734400-90735200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:90734400-90735200	Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr10:90734400-90735200	Active TSS	Ovary	ovary
8	chr10:90734400-90735200	Active TSS	Right Atrium	heart
9	chr10:90734400-90735200	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr10:90734400-90735200	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr10:90734400-90735400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr10:90734400-90735400	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr10:90734400-90735400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr10:90734400-90735400	Active TSS	Brain Hippocampus Middle	brain
15	chr10:90734400-90735400	Active TSS	Brain Substantia Nigra	brain
16	chr10:90734400-90735400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr10:90734400-90735400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr10:90734400-90735400	Active TSS	Psoas Muscle	Psoas
19	chr10:90734400-90735400	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr10:90734400-90735400	Flanking Active TSS	Dnd41	blood
21	chr10:90734400-90735400	Active TSS	HSMMtube	muscle
22	chr10:90734400-90735600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr10:90734400-90735600	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr10:90734400-90735600	Active TSS	Brain Anterior Caudate	brain
25	chr10:90734400-90735600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:90734400-90735600	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr10:90734400-90735600	Active TSS	Stomach Smooth Muscle	stomach
28	chr10:90734400-90735600	Flanking Active TSS	HUVEC	blood vessel
29	chr10:90734600-90735000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr10:90734600-90735000	Active TSS	Primary B cells from cord blood	blood
31	chr10:90734600-90735000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:90734600-90735000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:90734600-90735000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr10:90734600-90735000	Active TSS	Fetal Intestine Small	intestine
35	chr10:90734600-90735000	Active TSS	Fetal Kidney	kidney
36	chr10:90734600-90735200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr10:90734600-90735200	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr10:90734600-90735200	Active TSS	Muscle Satellite Cultured Cells	--
39	chr10:90734600-90735200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr10:90734600-90735200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr10:90734600-90735200	Active TSS	Colonic Mucosa	Colon
42	chr10:90734600-90735200	Active TSS	Fetal Lung	lung
43	chr10:90734600-90735200	Active TSS	Fetal Muscle Trunk	muscle
44	chr10:90734600-90735200	Active TSS	Placenta	Placenta
45	chr10:90734600-90735200	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr10:90734600-90735200	Active TSS	A549	lung
47	chr10:90734600-90735200	Active TSS	HMEC	breast
48	chr10:90734600-90735200	Active TSS	HSMM	muscle
49	chr10:90734600-90735200	Flanking Active TSS	NH-A	brain
50	chr10:90734600-90735400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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