Variant report

Variant	rs4542816
Chromosome Location	chr2:11842426-11842427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10180912	0.81[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12052681	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12465629	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12465630	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12692445	0.85[AMR][1000 genomes]
rs13036247	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4389306	0.84[EUR][1000 genomes]
rs4668739	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4669772	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669774	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669775	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55823449	0.82[AFR][1000 genomes]
rs62116211	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6432230	0.86[CEU][hapmap]
rs6432231	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs6736021	0.89[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6749129	0.82[YRI][hapmap]
rs7597788	0.85[EUR][1000 genomes]
rs7598716	0.83[EUR][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
rs4542816	LPIN1	cis	cerebellum	SCAN
rs4542816	NBAS	cis	cerebellum	SCAN
rs4542816	LPIN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11836800-11843200	Enhancers	Placenta	Placenta
2	chr2:11837800-11843200	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr2:11837800-11845400	Weak transcription	Pancreas	Pancrea
4	chr2:11837800-11848200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:11838000-11843000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:11838000-11843200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:11838200-11843400	Weak transcription	HMEC	breast
8	chr2:11838400-11844000	Weak transcription	Lung	lung
9	chr2:11838400-11845000	Weak transcription	Brain Anterior Caudate	brain
10	chr2:11838600-11843400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:11838600-11848000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:11838800-11843400	Weak transcription	NH-A	brain
13	chr2:11839000-11843200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:11839000-11843400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:11839000-11843400	Weak transcription	NHLF	lung
16	chr2:11839000-11843600	Weak transcription	NHEK	skin
17	chr2:11839200-11843200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:11839200-11843600	Weak transcription	HSMMtube	muscle
19	chr2:11839400-11843200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:11839400-11843400	Weak transcription	HSMM	muscle
21	chr2:11839400-11843600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:11840200-11844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:11840800-11842600	Enhancers	Esophagus	oesophagus
24	chr2:11841000-11843000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:11841200-11842600	Weak transcription	Psoas Muscle	Psoas
26	chr2:11841200-11842800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:11841200-11842800	Enhancers	Primary hematopoietic stem cells	blood
28	chr2:11841200-11842800	Enhancers	Dnd41	blood
29	chr2:11841400-11842600	Enhancers	Fetal Thymus	thymus
30	chr2:11841400-11842800	Enhancers	Primary B cells from peripheral blood	blood
31	chr2:11841400-11842800	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr2:11841600-11842800	Bivalent Enhancer	HepG2	liver
33	chr2:11841600-11850000	Weak transcription	Brain Substantia Nigra	brain
34	chr2:11841600-11850000	Weak transcription	Ovary	ovary
35	chr2:11841600-11850200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:11841800-11842600	Enhancers	Primary B cells from cord blood	blood
37	chr2:11841800-11842600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:11841800-11845000	Enhancers	Osteobl	bone
39	chr2:11841800-11850200	Weak transcription	Brain Angular Gyrus	brain
40	chr2:11842000-11842600	Enhancers	GM12878-XiMat	blood
41	chr2:11842000-11842800	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr2:11842000-11842800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:11842200-11842600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:11842200-11842600	Enhancers	K562	blood
45	chr2:11842200-11847600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:11842400-11842600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr2:11842400-11842600	Enhancers	Spleen	Spleen
48	chr2:11842400-11843400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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