Variant report

Variant	rs4981016
Chromosome Location	chr12:121983465-121983466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs28373517	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28379971	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28397967	0.90[EUR][1000 genomes]
rs28451063	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28481788	0.89[EUR][1000 genomes]
rs28520411	0.80[EUR][1000 genomes]
rs28604990	0.85[CEU][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs28618294	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28620502	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28663167	0.85[CEU][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs28667673	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28671138	0.81[EUR][1000 genomes]
rs28687122	0.88[EUR][1000 genomes]
rs28728162	0.96[CEU][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28757753	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28845610	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4981000	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4981004	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4981013	0.93[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	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4981016	MLXIP	cis	parietal	SCAN
rs4981016	DYNLL1	cis	parietal	SCAN
rs4981016	TAOK3	cis	parietal	SCAN
rs4981016	ORAI1	cis	lymphoblastoid	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121976400-121986400	Weak transcription	Lung	lung
2	chr12:121976400-121986400	Weak transcription	Ovary	ovary
3	chr12:121976400-121990000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:121976400-122001200	Strong transcription	Dnd41	blood
5	chr12:121976600-121985000	Weak transcription	Brain Angular Gyrus	brain
6	chr12:121976600-121986000	Weak transcription	Brain Substantia Nigra	brain
7	chr12:121976600-121986400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:121976600-121986400	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:121976600-121987200	Weak transcription	Aorta	Aorta
10	chr12:121976600-121988400	Weak transcription	Osteobl	bone
11	chr12:121976600-121988800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:121976600-121989800	Weak transcription	HSMMtube	muscle
13	chr12:121976600-122006800	Weak transcription	Fetal Lung	lung
14	chr12:121976600-122014600	Weak transcription	Colonic Mucosa	Colon
15	chr12:121976800-121983800	Weak transcription	Esophagus	oesophagus
16	chr12:121976800-121984600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:121976800-121984800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:121976800-121984800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:121976800-121984800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:121976800-121984800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:121976800-121984800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:121976800-121986200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:121976800-121986400	Weak transcription	Adipose Nuclei	Adipose
24	chr12:121976800-121986400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:121976800-121986400	Weak transcription	Left Ventricle	heart
26	chr12:121976800-121988400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:121976800-121988600	Weak transcription	Fetal Brain Female	brain
28	chr12:121976800-121990600	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:121976800-121995400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:121976800-121998600	Weak transcription	NHDF-Ad	bronchial
31	chr12:121977000-121983600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:121977000-121984600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:121977000-121984600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:121977000-121984600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:121977000-121984600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:121977000-121984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:121977000-121985000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr12:121977000-121986200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr12:121977000-121986200	Weak transcription	Right Ventricle	heart
40	chr12:121977000-121986200	Weak transcription	NHEK	skin
41	chr12:121977000-121986400	Weak transcription	Gastric	stomach
42	chr12:121977000-121986400	Weak transcription	Pancreas	Pancrea
43	chr12:121977000-121986400	Weak transcription	Spleen	Spleen
44	chr12:121977000-121986400	Weak transcription	NHLF	lung
45	chr12:121977000-121988200	Weak transcription	Liver	Liver
46	chr12:121977000-121989400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:121977000-121990600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:121977200-121983600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:121977200-121983600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:121977200-121984800	Weak transcription	Primary T cells from cord blood	blood

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