Variant report

Variant	rs62343367
Chromosome Location	chr5:9173601-9173602
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCT5-27	chr5:9173445-9173742	NONHSAT100331

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10039094	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10039096	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044766	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475457	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10475458	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11948082	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11952859	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11960524	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13354182	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13356945	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13362456	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13436248	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13436321	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1806077	1.00[EUR][1000 genomes]
rs1806089	0.90[EUR][1000 genomes]
rs1806110	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1806125	0.90[EUR][1000 genomes]
rs2074608	0.90[EUR][1000 genomes]
rs3026340	0.90[EUR][1000 genomes]
rs3777276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777277	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777278	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777279	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777280	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777282	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797916	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797917	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797918	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797919	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797922	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797923	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797924	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797925	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797931	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797933	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797934	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797936	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3822769	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822770	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822773	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822774	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3822776	0.83[EUR][1000 genomes]
rs55980672	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56043446	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56334239	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56705339	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62343370	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6555595	0.90[EUR][1000 genomes]
rs72643788	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72643790	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72643791	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72643792	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72643793	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72643794	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	21 gene(s)	inside rSNPs	diseases
2	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
8	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
9	nsv830200	chr5:9081023-9269495	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv597070	chr5:9100211-9280338	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv498044	chr5:9143754-9402870	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv530183	chr5:9146506-9413373	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9136800-9176400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:9136800-9189000	Weak transcription	Pancreas	Pancrea
3	chr5:9145600-9235400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:9153800-9183400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:9154000-9226200	Weak transcription	Fetal Intestine Large	intestine
6	chr5:9154800-9176200	Weak transcription	Fetal Intestine Small	intestine
7	chr5:9154800-9176400	Weak transcription	Aorta	Aorta
8	chr5:9155000-9174200	Weak transcription	Liver	Liver
9	chr5:9157600-9176400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:9163800-9189200	Weak transcription	Fetal Heart	heart
11	chr5:9165200-9185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:9166600-9176800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:9168800-9179800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:9169400-9173800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:9169400-9184600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr5:9169800-9202800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:9170000-9173800	Weak transcription	Brain Germinal Matrix	brain
18	chr5:9170000-9184400	Weak transcription	Fetal Lung	lung
19	chr5:9170800-9177800	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:9171000-9192000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:9171200-9173800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:9171400-9174200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:9171800-9174200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:9172000-9176000	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:9172200-9175200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:9172200-9176400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:9172200-9176800	Weak transcription	Fetal Stomach	stomach
28	chr5:9172400-9174200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:9172400-9174400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:9173200-9174000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr5:9173200-9175000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:9173200-9175000	Enhancers	NHEK	skin
33	chr5:9173400-9174800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:9173400-9174800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:9173400-9175000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:9173400-9175200	Enhancers	HMEC	breast
37	chr5:9173400-9175600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:9173400-9175600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr5:9173400-9176000	Enhancers	NHDF-Ad	bronchial
40	chr5:9173600-9173800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:9173600-9173800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr5:9173600-9174200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:9173600-9175200	Enhancers	NH-A	brain
44	chr5:9173600-9175600	Enhancers	Osteobl	bone
45	chr5:9173600-9175800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:9173600-9176000	Enhancers	NHLF	lung

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