Variant report

Variant	rs1299588
Chromosome Location	chr11:101874751-101874752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10791545	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10791546	0.85[ASN][1000 genomes]
rs10791548	0.81[ASN][1000 genomes]
rs10791549	0.80[ASN][1000 genomes]
rs10895220	0.85[CHB][hapmap]
rs10895228	0.86[ASN][1000 genomes]
rs10895231	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11225049	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs11225070	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11225080	0.85[ASN][1000 genomes]
rs11225087	0.87[ASN][1000 genomes]
rs11225093	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12281520	0.85[ASN][1000 genomes]
rs1274898	0.93[ASN][1000 genomes]
rs1274903	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1274904	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12802591	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1298710	0.94[ASN][1000 genomes]
rs1372414	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1441929	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1622630	0.92[ASN][1000 genomes]
rs1661409	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs1661410	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs1661411	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1661415	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1783740	0.91[CHB][hapmap]
rs2119734	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2282612	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs4643040	0.84[ASN][1000 genomes]
rs6590940	0.90[ASN][1000 genomes]
rs6590941	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs68066934	0.88[ASN][1000 genomes]
rs7107662	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7122772	0.83[ASN][1000 genomes]
rs975810	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][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	esv3362945	chr11:101736547-102114246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv898333	chr11:101832670-102079986	Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1299588	RICTOR	trans	parietal	SCAN
rs1299588	MMP1	cis	parietal	SCAN
rs1299588	KIAA1377	cis	parietal	SCAN
rs1299588	KIAA1377	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101821200-101878400	Weak transcription	Brain Anterior Caudate	brain
2	chr11:101827200-101883400	Weak transcription	Aorta	Aorta
3	chr11:101834600-101876000	Weak transcription	Fetal Lung	lung
4	chr11:101851600-101878200	Weak transcription	HUVEC	blood vessel
5	chr11:101852200-101874800	Weak transcription	Brain Hippocampus Middle	brain
6	chr11:101852800-101876000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:101854200-101874800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:101854400-101878200	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:101854800-101877600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:101858400-101878200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:101859400-101878200	Weak transcription	NHLF	lung
12	chr11:101859600-101878400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:101863600-101878200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:101864000-101878200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:101864200-101878200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:101864200-101878200	Weak transcription	Fetal Brain Female	brain
17	chr11:101864200-101878400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:101866600-101878400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:101867000-101880800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:101867400-101878000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr11:101869200-101878200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:101869200-101881400	Weak transcription	Adipose Nuclei	Adipose
23	chr11:101869400-101878400	Weak transcription	Ovary	ovary
24	chr11:101873000-101880800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:101873200-101878200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:101873200-101878400	Weak transcription	NHDF-Ad	bronchial
27	chr11:101873400-101881400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:101874200-101877600	Weak transcription	Hela-S3	cervix

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