Variant report

Variant	rs4145944
Chromosome Location	chr4:47593283-47593284
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10004474	0.91[ASN][1000 genomes]
rs10009447	0.91[ASN][1000 genomes]
rs10009857	0.91[ASN][1000 genomes]
rs10014808	0.91[ASN][1000 genomes]
rs10017276	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs10023715	0.91[ASN][1000 genomes]
rs10029782	0.91[ASN][1000 genomes]
rs10212847	0.88[JPT][hapmap]
rs10212955	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs10213076	1.00[JPT][hapmap]
rs10213618	1.00[JPT][hapmap]
rs11947521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331236	1.00[JPT][hapmap]
rs12331639	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12332008	0.88[ASN][1000 genomes]
rs12502587	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12504395	1.00[JPT][hapmap]
rs12509275	0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs13101892	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs13105718	0.90[JPT][hapmap]
rs13107754	1.00[JPT][hapmap]
rs13117568	0.91[ASN][1000 genomes]
rs13119296	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs13133133	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13133683	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13142266	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs13144815	0.91[ASN][1000 genomes]
rs13150235	0.82[ASW][hapmap]
rs13151904	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13152624	0.91[ASN][1000 genomes]
rs1317158	1.00[JPT][hapmap]
rs1317606	1.00[JPT][hapmap]
rs1344122	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs1578977	1.00[JPT][hapmap]
rs16860446	0.91[ASN][1000 genomes]
rs16860451	0.91[ASN][1000 genomes]
rs17462424	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17462541	0.91[ASN][1000 genomes]
rs17462720	0.91[JPT][hapmap]
rs17572095	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17572345	0.91[ASN][1000 genomes]
rs2351787	0.91[ASN][1000 genomes]
rs2351790	0.82[ASW][hapmap]
rs28424168	0.85[ASN][1000 genomes]
rs28455914	0.95[ASN][1000 genomes]
rs28539362	0.91[ASN][1000 genomes]
rs34048353	0.91[ASN][1000 genomes]
rs34088862	0.91[ASN][1000 genomes]
rs34996787	0.91[ASN][1000 genomes]
rs3811829	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4464539	0.91[ASN][1000 genomes]
rs4464540	0.91[ASN][1000 genomes]
rs4499673	1.00[JPT][hapmap]
rs4586905	1.00[JPT][hapmap]
rs4694861	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4694863	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4695252	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4695253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695254	0.91[ASN][1000 genomes]
rs4695255	0.88[ASN][1000 genomes]
rs4695260	1.00[JPT][hapmap]
rs4695264	1.00[JPT][hapmap]
rs5026274	0.91[ASN][1000 genomes]
rs56402433	0.91[ASN][1000 genomes]
rs66911545	0.91[ASN][1000 genomes]
rs6823760	0.92[ASN][1000 genomes]
rs6833737	0.91[ASN][1000 genomes]
rs6839273	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6839636	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs73238612	0.89[ASN][1000 genomes]
rs73238613	0.91[ASN][1000 genomes]
rs7657029	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7657209	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs7658554	1.00[JPT][hapmap]
rs7660901	1.00[JPT][hapmap]
rs7667912	0.91[ASN][1000 genomes]
rs7673289	0.88[ASN][1000 genomes]
rs7673938	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7695942	0.83[JPT][hapmap]
rs7697211	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs7699028	0.91[ASN][1000 genomes]
rs7699738	0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs9291308	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9291309	1.00[JPT][hapmap]
rs9291310	0.92[JPT][hapmap]
rs9291312	0.83[JPT][hapmap]
rs9291313	1.00[JPT][hapmap]
rs9993991	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9998849	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9998959	0.91[ASN][1000 genomes]
rs9999055	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829923	chr4:47436139-47678443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv998892	chr4:47493552-47863354	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv537081	chr4:47493552-47863354	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4145944	NIPAL1	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47555800-47594800	Weak transcription	Stomach Mucosa	stomach
2	chr4:47567600-47598400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:47568200-47595800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:47570400-47595400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:47570800-47595800	Strong transcription	Osteobl	bone
6	chr4:47570800-47596000	Strong transcription	Placenta	Placenta
7	chr4:47573400-47593600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:47574400-47595000	Weak transcription	Fetal Brain Female	brain
9	chr4:47575000-47610200	Weak transcription	Fetal Brain Male	brain
10	chr4:47581200-47595600	Weak transcription	HUVEC	blood vessel
11	chr4:47586200-47605400	Weak transcription	Fetal Stomach	stomach
12	chr4:47587800-47593600	Strong transcription	NH-A	brain
13	chr4:47587800-47594400	Strong transcription	Left Ventricle	heart
14	chr4:47587800-47595200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:47588000-47595200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:47589400-47593600	Strong transcription	Placenta Amnion	Placenta Amnion
17	chr4:47589800-47605400	Weak transcription	Gastric	stomach
18	chr4:47589800-47605400	Weak transcription	Spleen	Spleen
19	chr4:47590000-47594800	Weak transcription	Primary T cells from cord blood	blood
20	chr4:47590000-47595200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr4:47590000-47595600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:47590200-47601200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:47590600-47606000	Weak transcription	NHLF	lung
24	chr4:47590800-47600400	Weak transcription	Right Ventricle	heart
25	chr4:47591000-47593600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
26	chr4:47591400-47593400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:47591800-47593400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:47591800-47593400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr4:47591800-47593600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:47591800-47594200	Strong transcription	Ovary	ovary
31	chr4:47592000-47593400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:47592000-47593400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:47592000-47593400	ZNF genes & repeats	Liver	Liver
34	chr4:47592000-47593400	Strong transcription	Colonic Mucosa	Colon
35	chr4:47592000-47593600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
36	chr4:47592000-47593600	ZNF genes & repeats	Fetal Heart	heart
37	chr4:47592200-47593400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:47592200-47593400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:47592200-47593400	Strong transcription	Brain Cingulate Gyrus	brain
40	chr4:47592200-47593600	ZNF genes & repeats	Fetal Muscle Leg	muscle
41	chr4:47592200-47594200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:47592200-47594200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr4:47592200-47595000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr4:47592400-47593400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:47592400-47593400	ZNF genes & repeats	Aorta	Aorta
46	chr4:47592400-47593400	Strong transcription	Esophagus	oesophagus
47	chr4:47592400-47593400	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr4:47592400-47593400	ZNF genes & repeats	Fetal Lung	lung
49	chr4:47592400-47593400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr4:47592400-47593400	ZNF genes & repeats	HSMMtube	muscle

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