Variant report

Variant	rs17463666
Chromosome Location	chr4:47846701-47846702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NIPAL1-2	chr4:47841939-47846867	NONHSAT096267

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10028155	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10049713	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1062858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938499	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10938500	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938504	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938505	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938506	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12186152	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504018	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12506632	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12507439	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12510002	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12641871	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12651301	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1371729	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1371731	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1440221	0.84[EUR][1000 genomes]
rs1440228	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860663	0.84[EUR][1000 genomes]
rs17573709	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1822030	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1866689	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984713	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2033893	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2289435	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2352470	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28395298	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28412313	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28460483	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28573115	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583602	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28636596	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4565052	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695280	0.81[EUR][1000 genomes]
rs56001837	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447587	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447589	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6811177	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6823184	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823698	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6833758	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6858440	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180146	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978094	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9994561	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9995122	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9997555	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv829924	chr4:47670905-47866665	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv4328	chr4:47816467-47862253	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17463666	RP11-121C2.2	cis	Whole Blood	GTEx
rs17463666	CORIN	cis	Whole Blood	GTEx
rs17463666	CNGA1	cis	Muscle Skeletal	GTEx
rs17463666	CNGA1	cis	Adipose Subcutaneous	GTEx
rs17463666	NFXL1	cis	Whole Blood	GTEx
rs17463666	CNGA1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47838800-47859800	Weak transcription	Hela-S3	cervix
2	chr4:47839200-47850000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:47839200-47853800	Weak transcription	HSMMtube	muscle
4	chr4:47839800-47850000	Weak transcription	Gastric	stomach
5	chr4:47839800-47874800	Weak transcription	A549	lung
6	chr4:47839800-47875000	Weak transcription	Brain Angular Gyrus	brain
7	chr4:47839800-47885800	Weak transcription	Lung	lung
8	chr4:47840000-47848800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:47840000-47852600	Weak transcription	K562	blood
10	chr4:47840000-47852800	Weak transcription	Brain Anterior Caudate	brain
11	chr4:47840000-47854600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:47840000-47855600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:47840000-47874600	Weak transcription	Brain Substantia Nigra	brain
14	chr4:47840000-47874800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:47840000-47875400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:47840000-47875600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:47840000-47886800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:47840200-47849400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr4:47840200-47852800	Weak transcription	Fetal Kidney	kidney
20	chr4:47840200-47854000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:47840200-47855600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:47840200-47866600	Weak transcription	Esophagus	oesophagus
23	chr4:47840200-47867000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:47840200-47869600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:47840200-47874600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:47840200-47874800	Weak transcription	Psoas Muscle	Psoas
27	chr4:47840200-47881600	Weak transcription	Stomach Mucosa	stomach
28	chr4:47840200-47885200	Weak transcription	Aorta	Aorta
29	chr4:47840200-47885800	Weak transcription	Pancreas	Pancrea
30	chr4:47840400-47849400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:47840400-47849600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:47840400-47850000	Weak transcription	NH-A	brain
33	chr4:47840400-47853200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:47840400-47854200	Weak transcription	NHLF	lung
35	chr4:47840400-47855200	Weak transcription	Colonic Mucosa	Colon
36	chr4:47840400-47866600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:47840400-47874600	Weak transcription	Brain Hippocampus Middle	brain
38	chr4:47840400-47874600	Weak transcription	Fetal Brain Male	brain
39	chr4:47840400-47875400	Weak transcription	Small Intestine	intestine
40	chr4:47840400-47875600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:47840600-47855800	Weak transcription	Fetal Lung	lung
42	chr4:47840600-47874800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:47840600-47875200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:47840800-47867600	Weak transcription	Fetal Intestine Small	intestine
45	chr4:47840800-47874600	Weak transcription	Brain Germinal Matrix	brain
46	chr4:47840800-47874800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr4:47840800-47875400	Weak transcription	Right Ventricle	heart
48	chr4:47841200-47874800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:47841200-47874800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:47841400-47874600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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