Variant report

Variant	rs349027
Chromosome Location	chr19:44323949-44323950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44171987..44174273-chr19:44322847..44324891,2	K562	blood:
2	chr19:44323198..44325701-chr19:44330167..44332994,2	K562	blood:

Variant related genes	Relation type
ENSG00000167637	Chromatin interaction
ENSG00000159871	Chromatin interaction
ENSG00000011422	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10407794	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12459186	0.82[AMR][1000 genomes]
rs1865108	1.00[ASW][hapmap];0.86[CEU][hapmap]
rs189445	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033492	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2195980	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239947	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34424221	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs349026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs349031	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs349035	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs349036	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs349037	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs349054	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs349056	0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs365785	0.81[ASN][1000 genomes]
rs379758	1.00[ASW][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs443389	0.81[AMR][1000 genomes]
rs7251009	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7258953	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs349027	KCNN4	cis	multi-tissue	Pritchard
rs349027	FPR1	cis	parietal	SCAN
rs349027	ZNF283	trans	parietal	SCAN
rs349027	SIGLEC12	cis	parietal	SCAN
rs349027	ZNF283	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44319400-44324200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:44321800-44324000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:44321800-44324200	Weak transcription	HSMMtube	muscle
4	chr19:44322200-44324200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr19:44322200-44324200	Enhancers	NHEK	skin
6	chr19:44322800-44324200	Weak transcription	Esophagus	oesophagus
7	chr19:44323600-44324400	Weak transcription	Ovary	ovary
8	chr19:44323800-44324000	Active TSS	Brain Angular Gyrus	brain
9	chr19:44323800-44324000	Enhancers	Brain Anterior Caudate	brain
10	chr19:44323800-44324000	Enhancers	Brain Hippocampus Middle	brain
11	chr19:44323800-44324200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr19:44323800-44324400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr19:44323800-44324800	ZNF genes & repeats	Spleen	Spleen

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