Variant report

Variant	rs62076141
Chromosome Location	chr17:45933423-45933424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr17:45932850-45933574	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr17:45933175-45933463	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr17:45933072-45933574	HUVEC	blood vessel:	n/a	n/a
4	REST	chr17:45932985-45933525	PFSK-1	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:45927036..45931880-chr17:45931939..45936922,11	K562	blood:
2	chr17:45931856..45934572-chr17:45940574..45944336,3	K562	blood:
3	chr17:45931240..45934148-chr17:45971745..45974291,3	MCF-7	breast:
4	chr17:45908091..45909989-chr17:45932469..45934712,2	K562	blood:
5	chr17:45927380..45931249-chr17:45931939..45938449,12	K562	blood:
6	chr17:45932084..45934510-chr17:46047359..46049635,2	K562	blood:

No data

Variant related genes	Relation type
SP6	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000264243	Chromatin interaction
ENSG00000264920	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16948835	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2875737	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55919794	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066131	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503885	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72833458	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72833461	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8080650	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs878295	0.80[EUR][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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62076141	LRRC46	cis	Esophagus Muscularis	GTEx
rs62076141	LRRC46	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45929800-45940000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr17:45930800-45935600	Weak transcription	K562	blood
3	chr17:45932200-45933600	Bivalent Enhancer	Fetal Muscle Leg	muscle
4	chr17:45932800-45934400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:45933000-45933600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr17:45933000-45933600	Flanking Active TSS	HUVEC	blood vessel
7	chr17:45933000-45933800	Bivalent Enhancer	Adipose Nuclei	Adipose
8	chr17:45933000-45933800	Bivalent Enhancer	Fetal Heart	heart
9	chr17:45933000-45934200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr17:45933000-45935200	Enhancers	Placenta	Placenta
11	chr17:45933200-45933600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:45933200-45933800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr17:45933200-45934400	Enhancers	Lung	lung
14	chr17:45933200-45935600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:45933200-45935600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr17:45933400-45933600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
17	chr17:45933400-45933600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
18	chr17:45933400-45933600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
19	chr17:45933400-45933600	Bivalent Enhancer	Fetal Stomach	stomach
20	chr17:45933400-45934200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
21	chr17:45933400-45934600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:45933400-45937000	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links