Variant report

Variant	rs11840006
Chromosome Location	chr13:49203434-49203435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1009717	0.97[ASN][1000 genomes]
rs1009718	0.97[ASN][1000 genomes]
rs12867213	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12874937	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12876715	0.86[EUR][1000 genomes]
rs1359108	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1359109	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1575920	0.97[ASN][1000 genomes]
rs1854017	0.97[ASN][1000 genomes]
rs1980838	0.81[EUR][1000 genomes]
rs1980839	0.81[EUR][1000 genomes]
rs2146861	0.81[EUR][1000 genomes]
rs2406937	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2406938	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406939	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35109670	0.87[ASN][1000 genomes]
rs4451857	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59927903	0.86[EUR][1000 genomes]
rs6561469	0.97[ASN][1000 genomes]
rs6561471	0.86[ASN][1000 genomes]
rs6561474	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7324562	0.96[ASN][1000 genomes]
rs7332030	0.85[ASN][1000 genomes]
rs7989287	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7990619	0.97[ASN][1000 genomes]
rs7990660	0.97[ASN][1000 genomes]
rs8001736	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8002035	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535059	0.83[ASN][1000 genomes]
rs9535060	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562833	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568056	0.97[ASN][1000 genomes]
rs9568058	0.97[ASN][1000 genomes]
rs9568059	0.82[ASN][1000 genomes]
rs9568061	0.97[ASN][1000 genomes]
rs9568062	0.97[ASN][1000 genomes]
rs9568064	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9568065	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568066	0.86[EUR][1000 genomes]
rs9568069	0.85[ASN][1000 genomes]
rs9568070	0.86[EUR][1000 genomes]
rs9568072	0.85[EUR][1000 genomes]
rs9591187	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9595943	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9595944	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9595945	0.85[ASN][1000 genomes]
rs9595950	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3495983	chr13:49181790-49222165	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3495984	chr13:49181790-49222165	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11840006	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs11840006	LPAR6	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49196800-49205600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:49198000-49205000	Enhancers	Fetal Intestine Large	intestine
3	chr13:49199000-49205000	Enhancers	Fetal Intestine Small	intestine
4	chr13:49199800-49204200	Weak transcription	Aorta	Aorta
5	chr13:49201000-49207400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:49201200-49205200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr13:49201600-49205200	Weak transcription	Adipose Nuclei	Adipose
8	chr13:49201600-49210200	Weak transcription	Fetal Kidney	kidney
9	chr13:49202000-49203600	Weak transcription	Ovary	ovary
10	chr13:49202000-49204000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr13:49202000-49204200	Weak transcription	Left Ventricle	heart
12	chr13:49202000-49204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr13:49202000-49204800	Weak transcription	Placenta	Placenta
14	chr13:49202000-49205000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:49202000-49205000	Weak transcription	Right Atrium	heart
16	chr13:49202200-49208600	Weak transcription	Dnd41	blood
17	chr13:49202200-49210400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr13:49202400-49205000	Enhancers	Stomach Mucosa	stomach
19	chr13:49202800-49208800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:49203200-49203600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr13:49203200-49203600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr13:49203200-49204000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr13:49203200-49204000	Flanking Active TSS	HepG2	liver
24	chr13:49203200-49205400	Enhancers	Pancreas	Pancrea
25	chr13:49203400-49203800	Flanking Active TSS	Duodenum Mucosa	Duodenum

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