Variant report

Variant	rs61745825
Chromosome Location	chr1:214656476-214656477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USH2A-4	chr1:214655882-214656819	NONHSAT009463
2	lnc-USH2A-4	chr1:214656156-214656730	NONHSAT009464

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10158378	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158490	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159086	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159464	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12732499	1.00[AFR][1000 genomes]
rs12740482	1.00[AFR][1000 genomes]
rs17732539	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17732675	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17790515	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17790562	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34415256	1.00[AFR][1000 genomes]
rs35226076	1.00[AFR][1000 genomes]
rs35646913	1.00[AFR][1000 genomes]
rs4584365	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs5024205	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57880156	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58530653	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60798187	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819590	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61819591	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61819594	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61819596	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61819600	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819616	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819617	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819618	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819620	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819621	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61819622	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819623	0.90[EUR][1000 genomes]
rs61819624	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819625	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819627	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819628	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819630	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819631	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819632	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819637	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74139884	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74139885	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74139887	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74139888	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74139889	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468094	chr1:214654965-214687725	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv549180	chr1:214654965-214687725	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv945284	chr1:214655593-214656804	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214641400-214667800	Weak transcription	Hela-S3	cervix
2	chr1:214645200-214656600	Weak transcription	Fetal Intestine Large	intestine
3	chr1:214645800-214666000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:214646000-214672200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:214647200-214661600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:214648000-214669400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:214649200-214660800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:214650200-214657400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:214650200-214658000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:214650200-214666000	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:214650600-214657400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:214650800-214657400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:214650800-214660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:214650800-214662600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:214651000-214656800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:214651000-214666400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:214651200-214657400	Weak transcription	Psoas Muscle	Psoas
18	chr1:214651200-214659400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:214651200-214664600	Weak transcription	Left Ventricle	heart
20	chr1:214651200-214665600	Weak transcription	NHLF	lung
21	chr1:214651200-214666000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:214651200-214666400	Weak transcription	Adipose Nuclei	Adipose
23	chr1:214651600-214661400	Weak transcription	Fetal Heart	heart
24	chr1:214651800-214656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:214651800-214658000	Weak transcription	NH-A	brain
26	chr1:214651800-214663000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:214651800-214665400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:214651800-214668000	Weak transcription	HSMMtube	muscle
29	chr1:214652000-214665800	Weak transcription	NHDF-Ad	bronchial
30	chr1:214652000-214666000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:214652200-214658000	Weak transcription	HSMM	muscle
32	chr1:214652200-214664800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:214652600-214657400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:214652600-214662000	Weak transcription	HUVEC	blood vessel
35	chr1:214654400-214677400	Weak transcription	Gastric	stomach
36	chr1:214654600-214658400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:214655400-214657200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:214655600-214656600	Enhancers	Stomach Mucosa	stomach
39	chr1:214655600-214657400	Enhancers	Osteobl	bone
40	chr1:214655600-214659000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:214655800-214656800	Enhancers	A549	lung
42	chr1:214655800-214658400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr1:214656000-214657000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:214656000-214658200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:214656200-214656600	Enhancers	Small Intestine	intestine
46	chr1:214656200-214656800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:214656200-214656800	Enhancers	HMEC	breast
48	chr1:214656200-214657400	Enhancers	Colon Smooth Muscle	Colon
49	chr1:214656200-214657600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:214656200-214658000	Enhancers	NHEK	skin

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