Variant report

Variant	rs13407481
Chromosome Location	chr2:11843707-11843708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11842746..11844710-chr2:11858311..11861205,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10084363	0.80[EUR][1000 genomes]
rs10164822	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10167619	0.81[EUR][1000 genomes]
rs10179409	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10182021	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10206665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10209047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11683832	0.81[AFR][1000 genomes]
rs11695074	0.83[CHD][hapmap]
rs13386239	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13387137	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13390584	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13398067	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13407243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426765	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13428600	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13431864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432334	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4622687	0.84[EUR][1000 genomes]
rs55773509	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57281558	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58196703	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59844400	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6432232	0.81[EUR][1000 genomes]
rs6432233	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs66763856	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6708244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6716051	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716192	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725991	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6736015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748533	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67979481	0.82[ASN][1000 genomes]
rs7560325	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7570592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573725	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7574891	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7580112	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588803	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7591517	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9287737	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9287738	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv469449	chr2:11808654-11854012	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv580972	chr2:11808654-11854012	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13407481	YWHAQ	cis	cerebellum	SCAN
rs13407481	LPIN1	cis	cerebellum	SCAN
rs13407481	RRM2	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11837800-11845400	Weak transcription	Pancreas	Pancrea
2	chr2:11837800-11848200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:11838400-11844000	Weak transcription	Lung	lung
4	chr2:11838400-11845000	Weak transcription	Brain Anterior Caudate	brain
5	chr2:11838600-11848000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:11840200-11844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:11841600-11850000	Weak transcription	Brain Substantia Nigra	brain
8	chr2:11841600-11850000	Weak transcription	Ovary	ovary
9	chr2:11841600-11850200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:11841800-11845000	Enhancers	Osteobl	bone
11	chr2:11841800-11850200	Weak transcription	Brain Angular Gyrus	brain
12	chr2:11842200-11847600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:11842600-11844800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:11842600-11844800	Enhancers	NHDF-Ad	bronchial
15	chr2:11842800-11844200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr2:11843200-11844400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:11843200-11844600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:11843200-11844600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:11843200-11845000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:11843200-11845600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:11843200-11847800	Weak transcription	Placenta	Placenta
22	chr2:11843400-11844200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:11843400-11844400	Enhancers	HMEC	breast
24	chr2:11843400-11844400	Enhancers	HSMM	muscle
25	chr2:11843400-11844600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:11843400-11844600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:11843400-11844600	Enhancers	Psoas Muscle	Psoas
28	chr2:11843400-11844600	Enhancers	NH-A	brain
29	chr2:11843400-11844600	Enhancers	NHLF	lung
30	chr2:11843400-11844800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:11843600-11844200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:11843600-11844400	Enhancers	NHEK	skin
33	chr2:11843600-11844600	Enhancers	HSMMtube	muscle
34	chr2:11843600-11845600	Weak transcription	Esophagus	oesophagus

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