Variant report

Variant	rs17462424
Chromosome Location	chr4:47598298-47598299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10004474	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10009447	0.91[ASN][1000 genomes]
rs10009857	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10014808	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10017276	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs10023715	0.80[AMR][1000 genomes];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[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331236	1.00[JPT][hapmap]
rs12331639	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12332008	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12502587	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12504395	1.00[JPT][hapmap]
rs12509275	0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs13101892	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13105718	0.90[JPT][hapmap]
rs13106043	0.81[MEX][hapmap]
rs13107754	1.00[JPT][hapmap]
rs13117568	0.91[ASN][1000 genomes]
rs13119296	0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13133133	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13133683	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13142266	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs13144815	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13151904	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13152624	0.80[AMR][1000 genomes];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];0.86[MEX][hapmap]
rs1578977	1.00[JPT][hapmap]
rs16860446	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16860451	0.80[AMR][1000 genomes];0.91[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	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28424168	0.85[ASN][1000 genomes]
rs28455914	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28539362	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34048353	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34088862	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34996787	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3811829	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4145944	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]
rs4298115	0.81[MEX][hapmap]
rs4464539	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4464540	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4499673	1.00[JPT][hapmap]
rs4586905	1.00[JPT][hapmap]
rs4694861	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4694863	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4695252	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4695253	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695254	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4695255	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4695260	1.00[JPT][hapmap]
rs4695264	1.00[JPT][hapmap]
rs5026274	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56402433	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs66911545	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6823760	0.92[ASN][1000 genomes]
rs6833737	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6839273	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6839636	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73238612	0.89[ASN][1000 genomes]
rs73238613	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7657029	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7657209	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7658554	1.00[JPT][hapmap]
rs7660901	1.00[JPT][hapmap]
rs7667912	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7673289	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7673938	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7686393	0.81[MEX][hapmap]
rs7695942	0.83[JPT][hapmap]
rs7697211	0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7699028	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7699738	0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs9291308	1.00[JPT][hapmap];0.80[AMR][1000 genomes];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	0.80[AMR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17462424	NIPAL1	cis	cerebellum	SCAN
rs17462424	GABRA2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47567600-47598400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:47575000-47610200	Weak transcription	Fetal Brain Male	brain
3	chr4:47586200-47605400	Weak transcription	Fetal Stomach	stomach
4	chr4:47589800-47605400	Weak transcription	Gastric	stomach
5	chr4:47589800-47605400	Weak transcription	Spleen	Spleen
6	chr4:47590200-47601200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:47590600-47606000	Weak transcription	NHLF	lung
8	chr4:47590800-47600400	Weak transcription	Right Ventricle	heart
9	chr4:47592600-47598600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:47592600-47599800	Weak transcription	NHEK	skin
11	chr4:47593400-47598600	Weak transcription	Fetal Intestine Small	intestine
12	chr4:47593400-47600400	Weak transcription	Aorta	Aorta
13	chr4:47593400-47600400	Weak transcription	Lung	lung
14	chr4:47593400-47601600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:47593400-47605400	Weak transcription	Pancreas	Pancrea
16	chr4:47593400-47608200	Weak transcription	Esophagus	oesophagus
17	chr4:47593400-47614200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:47593600-47599000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:47593600-47599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:47593600-47599800	Weak transcription	Fetal Heart	heart
21	chr4:47593600-47599800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:47593600-47601400	Weak transcription	Small Intestine	intestine
23	chr4:47593600-47602400	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:47594200-47598400	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:47594200-47601200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:47594200-47605400	Weak transcription	Brain Substantia Nigra	brain
27	chr4:47594200-47607000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:47594200-47608000	Weak transcription	Brain Anterior Caudate	brain
29	chr4:47594200-47610200	Weak transcription	Ovary	ovary
30	chr4:47594200-47614400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:47594200-47614600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:47594400-47599800	Weak transcription	Left Ventricle	heart
33	chr4:47594400-47602000	Weak transcription	Fetal Intestine Large	intestine
34	chr4:47594400-47607000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:47594400-47607400	Weak transcription	HSMMtube	muscle
36	chr4:47594600-47606000	Weak transcription	Fetal Lung	lung
37	chr4:47594800-47600200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:47594800-47605000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:47594800-47606800	Weak transcription	Primary B cells from cord blood	blood
40	chr4:47595000-47598800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:47595000-47599400	Weak transcription	HMEC	breast
42	chr4:47595000-47601600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:47595000-47602200	Weak transcription	Dnd41	blood
44	chr4:47595000-47603600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr4:47595000-47607000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:47595200-47599200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:47595200-47604800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:47595400-47605600	Weak transcription	Liver	Liver
49	chr4:47595800-47598800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr4:47595800-47605400	Weak transcription	Osteobl	bone

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