Variant report

Variant	rs28466887
Chromosome Location	chr12:123911789-123911790
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1706477	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2137558	0.82[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs28384208	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28478828	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28576315	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28659953	0.85[EUR][1000 genomes]
rs28699127	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28817269	0.85[EUR][1000 genomes]
rs28838663	0.88[ASN][1000 genomes]
rs28886709	0.94[EUR][1000 genomes]
rs56042759	0.94[EUR][1000 genomes]
rs56309603	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs28466887	MSI1	cis	cerebellum	SCAN
rs28466887	RILPL2	cis	multi-tissue	Pritchard
rs28466887	PITPNM2	cis	cerebellum	SCAN
rs28466887	ENSG00000150977	cis	multi-tissue	Pritchard
rs28466887	WDR66	cis	parietal	SCAN
rs28466887	RILPL2	cis	lymphoblastoid	seeQTL
rs28466887	MGC7036	Cis_1M	lymphoblastoid	RTeQTL
rs28466887	C12orf65	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123889600-123917000	Weak transcription	K562	blood
2	chr12:123890800-123917200	Weak transcription	Fetal Kidney	kidney
3	chr12:123891200-123920400	Weak transcription	Psoas Muscle	Psoas
4	chr12:123891600-123919800	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:123891600-123920000	Weak transcription	Small Intestine	intestine
6	chr12:123892200-123916800	Weak transcription	NHEK	skin
7	chr12:123892200-123920200	Weak transcription	NH-A	brain
8	chr12:123892800-123920000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:123893400-123918200	Weak transcription	Hela-S3	cervix
10	chr12:123894000-123920600	Weak transcription	HSMMtube	muscle
11	chr12:123894200-123917000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:123894200-123917000	Weak transcription	HUVEC	blood vessel
13	chr12:123894800-123920000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:123895200-123918200	Weak transcription	Pancreas	Pancrea
15	chr12:123895200-123920000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:123895200-123920000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:123895200-123920000	Weak transcription	HSMM	muscle
18	chr12:123895200-123920000	Weak transcription	NHLF	lung
19	chr12:123895200-123920200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:123895200-123920200	Weak transcription	A549	lung
21	chr12:123896200-123911800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:123896200-123915600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr12:123896200-123915800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:123896400-123916200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:123899600-123916000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:123900600-123913000	Weak transcription	HepG2	liver
27	chr12:123903200-123917200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:123905600-123916800	Weak transcription	HMEC	breast
29	chr12:123905800-123918200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:123907400-123913000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:123907600-123911800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:123907600-123911800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:123907600-123913000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:123907600-123913000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:123907600-123915000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:123907600-123916800	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:123907600-123916800	Weak transcription	NHDF-Ad	bronchial
38	chr12:123907600-123917000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:123907600-123917200	Weak transcription	Gastric	stomach
40	chr12:123907600-123920000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:123907600-123920200	Weak transcription	Placenta	Placenta
42	chr12:123907600-123920200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:123907800-123911800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:123907800-123920000	Weak transcription	Fetal Muscle Leg	muscle
45	chr12:123908400-123913000	Weak transcription	Primary T cells from cord blood	blood
46	chr12:123908600-123918200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:123908600-123920200	Weak transcription	Fetal Intestine Small	intestine
48	chr12:123909800-123914800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:123910800-123913600	Strong transcription	Dnd41	blood
50	chr12:123910800-123915600	Strong transcription	Aorta	Aorta

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