Variant report

Variant	rs4803646
Chromosome Location	chr19:44133648-44133649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44076171..44077676-chr19:44133268..44135253,2	K562	blood:
2	chr19:44122314..44129769-chr19:44133350..44139066,11	MCF-7	breast:
3	chr19:44132706..44137711-chr19:44141592..44145407,6	K562	blood:

Variant related genes	Relation type
ENSG00000105767	Chromatin interaction
ENSG00000131116	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10402946	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13343696	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17655646	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184239	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs2030404	0.88[CHD][hapmap]
rs2240633	0.82[CEU][hapmap]
rs2270075	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599462	0.88[CHD][hapmap]
rs2682563	0.88[CHD][hapmap]
rs2682585	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs2682586	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2854501	0.87[CHD][hapmap]
rs2854506	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs2854508	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs2854509	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs304719	0.82[CEU][hapmap]
rs304720	0.82[CEU][hapmap]
rs304722	0.85[CEU][hapmap]
rs304723	0.82[CEU][hapmap]
rs304731	1.00[CHB][hapmap]
rs3213255	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs3213263	0.83[CHD][hapmap]
rs3213334	0.88[CHD][hapmap]
rs3213356	0.88[CHD][hapmap]
rs34163641	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34637472	0.82[CEU][hapmap]
rs365063	0.82[CEU][hapmap]
rs427115	0.82[CEU][hapmap]
rs7251275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs762506	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs762507	0.88[CHD][hapmap]
rs8101956	0.82[CEU][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4803646	PLAUR	cis	multi-tissue	Pritchard
rs4803646	STRN4	cis	cerebellum	SCAN
rs4803646	ELSPBP1	cis	cerebellum	SCAN
rs4803646	ETHE1	cis	lymphoblastoid	seeQTL
rs4803646	XRCC1	cis	lymphoblastoid	seeQTL
rs4803646	CCDC8	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44124600-44143400	Weak transcription	Right Atrium	heart
2	chr19:44124800-44138400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr19:44124800-44138800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:44124800-44139000	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:44125000-44139200	Weak transcription	Pancreas	Pancrea
6	chr19:44125200-44137400	Weak transcription	HepG2	liver
7	chr19:44125800-44135400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:44126600-44134000	Strong transcription	Brain Germinal Matrix	brain
9	chr19:44128600-44138800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:44129000-44138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:44129200-44138200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr19:44130800-44138400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:44131000-44138800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:44131200-44138200	Weak transcription	Esophagus	oesophagus
15	chr19:44131200-44139400	Weak transcription	Spleen	Spleen
16	chr19:44131400-44133800	Enhancers	Brain Hippocampus Middle	brain
17	chr19:44131400-44137000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:44131400-44138400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:44131400-44138400	Weak transcription	Fetal Stomach	stomach
20	chr19:44131400-44138800	Weak transcription	Fetal Intestine Small	intestine
21	chr19:44131600-44138200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:44131600-44138400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:44131800-44135000	Enhancers	Brain Substantia Nigra	brain
24	chr19:44131800-44138800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr19:44131800-44139000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:44132000-44134800	Weak transcription	Fetal Brain Female	brain
27	chr19:44132000-44136200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:44132000-44137600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:44132000-44138400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:44132000-44138800	Weak transcription	K562	blood
31	chr19:44133200-44134600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:44133200-44137600	Weak transcription	Brain Anterior Caudate	brain
33	chr19:44133400-44134200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:44133600-44137400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr19:44133600-44138000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:44133600-44138200	Weak transcription	Brain Angular Gyrus	brain
37	chr19:44133600-44138200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links