Variant report

Variant	rs400058
Chromosome Location	chr19:44141015-44141016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44139192..44141813-chr19:44144492..44146172,2	MCF-7	breast:
2	chr19:44118551..44131201-chr19:44135615..44147023,20	K562	blood:
3	chr19:44121917..44126953-chr19:44140515..44144634,11	MCF-7	breast:
4	chr19:44131994..44133560-chr19:44140459..44143451,2	MCF-7	breast:
5	chr19:44098885..44105672-chr19:44139703..44145307,6	MCF-7	breast:
6	chr19:44140278..44143480-chr19:44195245..44198704,3	K562	blood:

Variant related genes	Relation type
ENSG00000131116	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000105767	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7252391	0.88[ASW][hapmap]

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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs400058	LIPJ	trans	cerebellum	SCAN
rs400058	SLC6A16	cis	cerebellum	SCAN
rs400058	PRRG2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44124600-44143400	Weak transcription	Right Atrium	heart
2	chr19:44137400-44142600	Enhancers	Fetal Brain Male	brain
3	chr19:44139000-44142800	Weak transcription	Esophagus	oesophagus
4	chr19:44139600-44142600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:44139800-44141400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:44139800-44141800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:44139800-44143400	Weak transcription	Ovary	ovary
8	chr19:44140000-44141600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:44140000-44142400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr19:44140000-44143200	Weak transcription	Right Ventricle	heart
11	chr19:44140200-44141400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr19:44140400-44141400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:44140400-44142200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:44140400-44142400	Weak transcription	Pancreas	Pancrea
15	chr19:44140600-44143000	Weak transcription	Fetal Heart	heart
16	chr19:44140800-44141200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr19:44140800-44141200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr19:44140800-44141200	Active TSS	Fetal Brain Female	brain
19	chr19:44140800-44141400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr19:44140800-44141400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr19:44140800-44141600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:44140800-44142200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:44140800-44142200	Enhancers	Brain Hippocampus Middle	brain
24	chr19:44140800-44142400	Enhancers	Brain Angular Gyrus	brain
25	chr19:44140800-44142400	Enhancers	Brain Cingulate Gyrus	brain
26	chr19:44140800-44142400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:44140800-44142600	Enhancers	Brain Substantia Nigra	brain
28	chr19:44140800-44142600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr19:44140800-44142600	Enhancers	HepG2	liver
30	chr19:44140800-44142800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:44141000-44141200	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr19:44141000-44141400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:44141000-44141800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:44141000-44142000	Flanking Active TSS	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links