Variant report

Variant	rs11947521
Chromosome Location	chr4:47593976-47593977
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

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];0.87[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]
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];0.91[MEX][hapmap]
rs13101892	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];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];0.80[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];0.87[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]
rs17462424	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]
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	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]
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];0.82[MEX][hapmap]
rs4695252	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4695253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[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];0.87[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]
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	0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11947521	NIPAL1	cis	cerebellum	SCAN

Chromatin state (count:86 , 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	chr4:47574400-47595000	Weak transcription	Fetal Brain Female	brain
8	chr4:47575000-47610200	Weak transcription	Fetal Brain Male	brain
9	chr4:47581200-47595600	Weak transcription	HUVEC	blood vessel
10	chr4:47586200-47605400	Weak transcription	Fetal Stomach	stomach
11	chr4:47587800-47594400	Strong transcription	Left Ventricle	heart
12	chr4:47587800-47595200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:47588000-47595200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:47589800-47605400	Weak transcription	Gastric	stomach
15	chr4:47589800-47605400	Weak transcription	Spleen	Spleen
16	chr4:47590000-47594800	Weak transcription	Primary T cells from cord blood	blood
17	chr4:47590000-47595200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:47590000-47595600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:47590200-47601200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:47590600-47606000	Weak transcription	NHLF	lung
21	chr4:47590800-47600400	Weak transcription	Right Ventricle	heart
22	chr4:47591800-47594200	Strong transcription	Ovary	ovary
23	chr4:47592200-47594200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:47592200-47594200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr4:47592200-47595000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr4:47592600-47595000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr4:47592600-47597600	Strong transcription	HSMM	muscle
28	chr4:47592600-47598600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr4:47592600-47599800	Weak transcription	NHEK	skin
30	chr4:47592800-47594000	Strong transcription	Brain Angular Gyrus	brain
31	chr4:47592800-47594200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:47592800-47594200	Strong transcription	Brain Anterior Caudate	brain
33	chr4:47592800-47594200	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr4:47592800-47594200	Strong transcription	Colon Smooth Muscle	Colon
35	chr4:47592800-47594200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr4:47592800-47594400	Strong transcription	Brain Hippocampus Middle	brain
37	chr4:47592800-47594400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:47592800-47594400	Strong transcription	Fetal Intestine Large	intestine
39	chr4:47592800-47594400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr4:47592800-47594800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:47592800-47594800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:47592800-47594800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr4:47592800-47595000	Strong transcription	Dnd41	blood
44	chr4:47592800-47595400	Strong transcription	Adipose Nuclei	Adipose
45	chr4:47592800-47595800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:47592800-47596800	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr4:47593000-47594200	Strong transcription	Brain Substantia Nigra	brain
48	chr4:47593000-47594600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:47593200-47594200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:47593200-47594800	Strong transcription	Primary B cells from cord blood	blood

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