Variant report

Variant	rs11172818
Chromosome Location	chr12:59298290-59298291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1020031	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10877182	1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10877183	1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10877185	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11172790	0.83[TSI][hapmap]
rs11172795	0.81[EUR][1000 genomes]
rs11172797	0.86[EUR][1000 genomes]
rs11172799	0.85[ASW][hapmap];0.87[YRI][hapmap]
rs11172801	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11172802	0.92[EUR][1000 genomes]
rs11172804	0.92[EUR][1000 genomes]
rs11172805	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11172806	0.89[EUR][1000 genomes]
rs11172807	0.92[EUR][1000 genomes]
rs11172808	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11172809	0.92[EUR][1000 genomes]
rs11172811	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11172812	1.00[EUR][1000 genomes]
rs11172816	1.00[EUR][1000 genomes]
rs11172817	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12146851	0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12303283	0.87[YRI][hapmap]
rs13377741	0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap]
rs17120227	0.95[EUR][1000 genomes]
rs17617428	0.81[EUR][1000 genomes]
rs2167030	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2279718	0.83[TSI][hapmap]
rs7303924	0.89[MKK][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11172818	CAPS	trans	brain	seeQTL
rs11172818	SLC47A2	trans	brain	seeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
2	chr12:59275000-59300800	Weak transcription	HSMMtube	muscle
3	chr12:59279000-59310800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:59279200-59309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:59283800-59300400	Weak transcription	Placenta	Placenta
6	chr12:59284000-59300800	Weak transcription	Colonic Mucosa	Colon
7	chr12:59284000-59300800	Weak transcription	HepG2	liver
8	chr12:59284200-59304600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:59287800-59301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:59288200-59298600	Weak transcription	NHLF	lung
11	chr12:59289200-59300800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:59289400-59301200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:59289600-59300800	Weak transcription	Aorta	Aorta
14	chr12:59289800-59300800	Weak transcription	Lung	lung
15	chr12:59289800-59304600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:59289800-59305400	Weak transcription	Spleen	Spleen
17	chr12:59290600-59300800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:59290600-59300800	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:59290600-59307200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:59290600-59311000	Weak transcription	Right Ventricle	heart
21	chr12:59291800-59302800	Weak transcription	Psoas Muscle	Psoas
22	chr12:59292000-59298400	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:59292000-59300800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:59292200-59300800	Weak transcription	Brain Substantia Nigra	brain
25	chr12:59292400-59309200	Weak transcription	Fetal Heart	heart
26	chr12:59292400-59310600	Weak transcription	Small Intestine	intestine
27	chr12:59292600-59301600	Weak transcription	Gastric	stomach
28	chr12:59292600-59303000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:59293000-59301200	Weak transcription	Esophagus	oesophagus
30	chr12:59293600-59300800	Weak transcription	Pancreas	Pancrea
31	chr12:59295400-59302800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr12:59296200-59299600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:59297800-59298400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr12:59297800-59298400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr12:59297800-59298400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:59297800-59298400	ZNF genes & repeats	NH-A	brain
37	chr12:59297800-59298600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:59297800-59298600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:59297800-59298600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:59297800-59299000	Strong transcription	Fetal Kidney	kidney
41	chr12:59297800-59299600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:59297800-59299800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:59297800-59299800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:59297800-59299800	Strong transcription	Adipose Nuclei	Adipose
45	chr12:59297800-59300000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:59297800-59300200	Strong transcription	HMEC	breast
47	chr12:59297800-59300400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:59297800-59300400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:59297800-59300800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:59297800-59300800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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