Variant report

Variant	rs1422075
Chromosome Location	chr5:114530301-114530302
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114528643..114531449-chr5:114541166..114543172,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PGGT1B-4	chr5:114530240-114530633	NONHSAT103295

Variant related genes	Relation type
ENSG00000248175	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10051090	0.80[ASN][1000 genomes]
rs10519400	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11241317	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12054867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1422074	0.83[ASN][1000 genomes]
rs1559080	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1990897	0.83[ASN][1000 genomes]
rs2112363	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7713151	0.83[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	nsv830453	chr5:114277261-114546536	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114522800-114543400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:114523400-114576200	Weak transcription	Psoas Muscle	Psoas
3	chr5:114525400-114531400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr5:114525800-114544800	Weak transcription	Primary T cells from cord blood	blood
5	chr5:114528000-114563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:114529200-114562600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:114529400-114531400	Enhancers	Stomach Mucosa	stomach
8	chr5:114529400-114532000	Enhancers	Duodenum Mucosa	Duodenum
9	chr5:114529600-114530400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr5:114529600-114531400	Enhancers	Liver	Liver
11	chr5:114529800-114531000	Enhancers	HepG2	liver
12	chr5:114529800-114551000	Weak transcription	Left Ventricle	heart
13	chr5:114530000-114530600	Enhancers	Pancreas	Pancrea
14	chr5:114530000-114530800	Enhancers	Adipose Nuclei	Adipose
15	chr5:114530000-114531000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:114530000-114531200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:114530200-114530600	Enhancers	Fetal Intestine Large	intestine
18	chr5:114530200-114530800	Enhancers	NHDF-Ad	bronchial
19	chr5:114530200-114531000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:114530200-114531000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:114530200-114531000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr5:114530200-114531000	Enhancers	Fetal Intestine Small	intestine
23	chr5:114530200-114562600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:114530200-114562600	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links