Variant report

Variant	rs72664354
Chromosome Location	chr1:57004417-57004418
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKAA2-9	chr1:57004124-57004583	NONHSAT003451

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17114036	0.88[EUR][1000 genomes]
rs17114046	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2404715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634932	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55869368	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56170783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56186267	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56322312	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56348932	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664318	0.88[EUR][1000 genomes]
rs72664324	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72664332	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664335	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664341	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664358	0.91[ASN][1000 genomes]
rs9970807	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv945965	chr1:57003085-57005467	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
2	chr1:56992800-57011200	Weak transcription	Stomach Mucosa	stomach
3	chr1:56993000-57004600	Weak transcription	Hela-S3	cervix
4	chr1:56993600-57007800	Weak transcription	Primary B cells from cord blood	blood
5	chr1:56994000-57012400	Weak transcription	Fetal Brain Male	brain
6	chr1:56994000-57012800	Weak transcription	Fetal Brain Female	brain
7	chr1:56995600-57004600	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:56996600-57005200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:56997200-57004600	Genic enhancers	Placenta	Placenta
10	chr1:56999400-57012800	Weak transcription	HSMMtube	muscle
11	chr1:57000200-57005000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:57000200-57008200	Weak transcription	Fetal Kidney	kidney
13	chr1:57000400-57011000	Weak transcription	Gastric	stomach
14	chr1:57000400-57013000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:57000600-57005400	Weak transcription	Colonic Mucosa	Colon
16	chr1:57001200-57018800	Weak transcription	A549	lung
17	chr1:57001400-57004600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:57001800-57018600	Weak transcription	Small Intestine	intestine
19	chr1:57001800-57021800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:57002400-57004600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:57002400-57005200	Weak transcription	Aorta	Aorta
22	chr1:57002400-57008600	Enhancers	Brain Hippocampus Middle	brain
23	chr1:57002600-57004600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:57002600-57005200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:57002600-57005200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:57002600-57006600	Enhancers	Right Atrium	heart
27	chr1:57002600-57008600	Enhancers	Brain Anterior Caudate	brain
28	chr1:57002800-57004600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:57002800-57004800	Weak transcription	Fetal Heart	heart
30	chr1:57002800-57006400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:57002800-57006600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr1:57002800-57006800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr1:57002800-57006800	Enhancers	Fetal Intestine Small	intestine
34	chr1:57002800-57013200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:57002800-57018600	Weak transcription	Thymus	Thymus
36	chr1:57003000-57004600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:57003000-57005000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:57003000-57006800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr1:57003000-57006800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr1:57003000-57007200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr1:57003000-57007600	Enhancers	Adipose Nuclei	Adipose
42	chr1:57003000-57008000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr1:57003000-57008600	Enhancers	H1 Cell Line	embryonic stem cell
44	chr1:57003200-57007600	Enhancers	Brain Substantia Nigra	brain
45	chr1:57003200-57007600	Enhancers	Fetal Lung	lung
46	chr1:57003200-57011400	Weak transcription	Lung	lung
47	chr1:57003200-57019800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:57003400-57006000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr1:57003400-57008600	Enhancers	Ovary	ovary
50	chr1:57003400-57015400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links