Variant report

Variant	rs58419446
Chromosome Location	chr1:150490370-150490371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150254103..150255766-chr1:150487973..150490880,2	MCF-7	breast:
2	chr1:150458274..150463765-chr1:150483214..150490747,8	K562	blood:
3	chr1:150488672..150491336-chr1:150533266..150536212,3	K562	blood:
4	chr1:150458065..150461622-chr1:150486691..150490573,5	MCF-7	breast:
5	chr1:150489113..150492818-chr1:150530627..150535563,5	K562	blood:
6	chr1:150488378..150490694-chr1:150500940..150503568,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ECM1-1	chr1:150490249-150490508	ENSG00000228126

No data

Variant related genes	Relation type
ENSG00000159208	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000203804	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs12116970	0.88[ASN][1000 genomes]
rs12129037	0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12718416	0.87[ASN][1000 genomes]
rs12729719	0.88[ASN][1000 genomes]
rs13057	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16830437	0.85[ASN][1000 genomes]
rs16835782	0.85[ASN][1000 genomes]
rs16835791	0.85[ASN][1000 genomes]
rs16835911	0.81[ASN][1000 genomes]
rs16836130	0.81[ASN][1000 genomes]
rs16836139	0.81[ASN][1000 genomes]
rs16836442	0.81[ASN][1000 genomes]
rs16836576	0.85[ASN][1000 genomes]
rs16836594	0.85[ASN][1000 genomes]
rs16836601	0.85[ASN][1000 genomes]
rs16836786	0.85[ASN][1000 genomes]
rs16836940	0.81[ASN][1000 genomes]
rs16836943	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2015966	0.81[ASN][1000 genomes]
rs2275245	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2275779	0.81[ASN][1000 genomes]
rs3737319	0.81[ASN][1000 genomes]
rs3738322	0.83[ASN][1000 genomes]
rs3806389	0.91[ASN][1000 genomes]
rs3850843	0.85[ASN][1000 genomes]
rs4926420	0.81[ASN][1000 genomes]
rs4926430	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4970925	0.91[ASN][1000 genomes]
rs4970927	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4970946	0.88[ASN][1000 genomes]
rs4970947	0.91[ASN][1000 genomes]
rs56882505	0.85[ASN][1000 genomes]
rs56909494	0.85[ASN][1000 genomes]
rs57163995	0.81[ASN][1000 genomes]
rs57272513	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57971032	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58516261	0.81[ASN][1000 genomes]
rs59367061	0.85[ASN][1000 genomes]
rs59378360	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs59639798	0.85[ASN][1000 genomes]
rs59662772	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60459288	0.85[ASN][1000 genomes]
rs60531845	0.81[ASN][1000 genomes]
rs60730811	0.81[ASN][1000 genomes]
rs66464034	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6680391	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs66866430	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6700009	0.81[ASN][1000 genomes]
rs71622690	0.81[ASN][1000 genomes]
rs72700806	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73013119	0.85[ASN][1000 genomes]
rs73013129	0.81[ASN][1000 genomes]
rs73015063	0.81[ASN][1000 genomes]
rs73015078	0.81[ASN][1000 genomes]
rs73015081	0.81[ASN][1000 genomes]
rs73015095	0.81[ASN][1000 genomes]
rs73015096	0.81[ASN][1000 genomes]
rs73017006	0.81[ASN][1000 genomes]
rs73017073	0.85[ASN][1000 genomes]
rs73017086	0.85[ASN][1000 genomes]
rs73017092	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73017102	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73019017	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73019018	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73019020	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73019021	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73019027	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73019028	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73019054	0.96[AFR][1000 genomes]
rs871527	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs953127	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[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	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
2	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
3	esv1814231	chr1:150479528-150540117	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150489000-150490800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:150489000-150494800	Weak transcription	Esophagus	oesophagus
3	chr1:150489000-150505400	Weak transcription	Right Ventricle	heart
4	chr1:150489200-150490400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:150489200-150490400	Enhancers	Primary B cells from cord blood	blood
6	chr1:150489200-150490400	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:150489200-150490400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:150489200-150490600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr1:150489200-150494400	Weak transcription	Psoas Muscle	Psoas
10	chr1:150489200-150498200	Weak transcription	Fetal Intestine Small	intestine
11	chr1:150489200-150501800	Weak transcription	Right Atrium	heart
12	chr1:150489400-150490400	Enhancers	GM12878-XiMat	blood
13	chr1:150489400-150497000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:150489400-150500200	Weak transcription	Osteobl	bone
15	chr1:150489400-150500400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:150489600-150490600	Enhancers	K562	blood
17	chr1:150489600-150498400	Weak transcription	Fetal Stomach	stomach
18	chr1:150489600-150501600	Weak transcription	Brain Anterior Caudate	brain
19	chr1:150489800-150490400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:150489800-150490400	Enhancers	Fetal Muscle Leg	muscle
21	chr1:150490000-150490400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:150490000-150490600	Enhancers	Stomach Mucosa	stomach
23	chr1:150490200-150490400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:150490200-150490400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:150490200-150490400	Enhancers	Liver	Liver
26	chr1:150490200-150490400	Enhancers	Brain Angular Gyrus	brain
27	chr1:150490200-150490400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr1:150490200-150490400	Enhancers	Spleen	Spleen
29	chr1:150490200-150494200	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links