Variant report

Variant	rs405424
Chromosome Location	chr1:86826469-86826470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL24A1-3	chr1:86826109-86826604	NONHSAT004266

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10493789	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10747328	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10873777	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1158505	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1182102	0.89[EUR][1000 genomes]
rs1334143	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1334146	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1334147	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1334148	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs166626	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs166627	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17129078	0.85[ASN][1000 genomes]
rs175363	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187971	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1931363	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2104962	0.83[AFR][1000 genomes]
rs2104963	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2151708	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2151709	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs272491	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272492	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272494	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272498	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272504	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs272507	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs272510	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272511	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs272516	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3765975	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs410807	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4288573	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs450927	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs452865	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs567133	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs569912	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61804060	0.85[ASN][1000 genomes]
rs6695671	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7527383	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs883200	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86808600-86842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:86813800-86836400	Weak transcription	Lung	lung
3	chr1:86813800-86842600	Weak transcription	Fetal Heart	heart
4	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
5	chr1:86816000-86842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:86817200-86843800	Weak transcription	Small Intestine	intestine
7	chr1:86817600-86843000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:86817800-86828000	Weak transcription	Fetal Stomach	stomach
9	chr1:86817800-86828000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:86817800-86835400	Weak transcription	Esophagus	oesophagus
11	chr1:86817800-86840000	Weak transcription	GM12878-XiMat	blood
12	chr1:86817800-86842400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:86818000-86842600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:86818000-86843200	Weak transcription	Pancreas	Pancrea
15	chr1:86818000-86851600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:86818200-86841000	Weak transcription	Fetal Kidney	kidney
17	chr1:86819000-86838400	Weak transcription	NHDF-Ad	bronchial
18	chr1:86819800-86828000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:86819800-86830200	Weak transcription	Spleen	Spleen
20	chr1:86819800-86839400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:86819800-86839400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:86819800-86840200	Weak transcription	Brain Angular Gyrus	brain
23	chr1:86819800-86840200	Weak transcription	HMEC	breast
24	chr1:86819800-86842200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:86819800-86842600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:86819800-86843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:86819800-86843000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:86820200-86826800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:86820200-86840200	Weak transcription	Brain Anterior Caudate	brain
30	chr1:86820200-86841200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:86820200-86842600	Weak transcription	Brain Germinal Matrix	brain
32	chr1:86820200-86843400	Weak transcription	Left Ventricle	heart
33	chr1:86820200-86854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:86820200-86854800	Weak transcription	HSMMtube	muscle
35	chr1:86820400-86835000	Weak transcription	HSMM	muscle
36	chr1:86820400-86838400	Weak transcription	Primary B cells from cord blood	blood
37	chr1:86820400-86838400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:86820400-86838400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:86820400-86838600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:86820400-86839400	Weak transcription	NH-A	brain
41	chr1:86820400-86842400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:86820400-86842800	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:86820400-86842800	Weak transcription	Placenta	Placenta
44	chr1:86820400-86845400	Weak transcription	Hela-S3	cervix
45	chr1:86820400-86846200	Weak transcription	NHLF	lung
46	chr1:86820400-86846400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:86820400-86847000	Weak transcription	Liver	Liver
48	chr1:86820400-86848000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:86820400-86860200	Weak transcription	NHEK	skin
50	chr1:86820600-86838400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links