Variant report

Variant	rs9548800
Chromosome Location	chr13:40105288-40105289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PROSER1-3	chr13:40100016-40107556	NONHSAT033305

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1885759	0.85[YRI][hapmap]
rs55783364	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7322336	0.83[AFR][1000 genomes]
rs7333056	1.00[YRI][hapmap]
rs7334594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7982917	0.89[ASW][hapmap];0.81[GIH][hapmap];0.87[YRI][hapmap]
rs9315702	0.89[ASW][hapmap];0.87[YRI][hapmap]
rs9315706	1.00[YRI][hapmap]
rs9532388	0.81[GIH][hapmap]
rs9548798	0.86[CEU][hapmap];0.98[GIH][hapmap]
rs9548819	0.81[GIH][hapmap]
rs9548822	0.86[AFR][1000 genomes]
rs9548824	0.82[AFR][1000 genomes]
rs9548825	0.81[GIH][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs9548826	1.00[YRI][hapmap]
rs9548827	1.00[YRI][hapmap]
rs9548829	1.00[YRI][hapmap];0.83[AFR][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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS 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	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1050137	chr13:40090742-40118499	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9548800	ELF1	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40096800-40110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:40099400-40106000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:40101600-40110400	Weak transcription	Psoas Muscle	Psoas
4	chr13:40102600-40110600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr13:40102800-40106000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:40102800-40106400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr13:40102800-40107600	Weak transcription	Ovary	ovary
8	chr13:40102800-40107800	Weak transcription	Fetal Brain Male	brain
9	chr13:40102800-40110400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr13:40102800-40110800	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:40102800-40111200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:40103000-40105800	Enhancers	NHDF-Ad	bronchial
13	chr13:40103000-40109000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr13:40103200-40105600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:40103200-40108400	Weak transcription	Fetal Brain Female	brain
16	chr13:40103200-40110800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:40103400-40105400	Weak transcription	HSMM	muscle
18	chr13:40103400-40105600	Weak transcription	Fetal Muscle Leg	muscle
19	chr13:40104000-40105600	Weak transcription	NH-A	brain
20	chr13:40104200-40105400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:40104400-40106200	Enhancers	Fetal Heart	heart
22	chr13:40104400-40106400	Enhancers	Right Atrium	heart
23	chr13:40104400-40106600	Enhancers	NHEK	skin
24	chr13:40104600-40105600	Weak transcription	Left Ventricle	heart
25	chr13:40104600-40105800	Weak transcription	Right Ventricle	heart
26	chr13:40104600-40106000	Enhancers	Osteobl	bone
27	chr13:40104600-40106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr13:40104800-40105400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr13:40104800-40105600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr13:40104800-40106000	Enhancers	Fetal Lung	lung
31	chr13:40104800-40106000	Enhancers	A549	lung
32	chr13:40104800-40106200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:40104800-40106200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr13:40104800-40106200	Enhancers	Adipose Nuclei	Adipose
35	chr13:40104800-40106200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr13:40104800-40106200	Enhancers	HSMMtube	muscle
37	chr13:40105000-40105400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr13:40105000-40105600	Enhancers	Brain Substantia Nigra	brain
39	chr13:40105000-40105800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr13:40105000-40106200	Enhancers	Colon Smooth Muscle	Colon
41	chr13:40105000-40106400	Enhancers	HMEC	breast
42	chr13:40105000-40106400	Enhancers	NHLF	lung
43	chr13:40105000-40106600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:40105000-40106600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr13:40105000-40106600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:40105000-40106600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr13:40105200-40105600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:40105200-40107200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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