Variant report

Variant	rs2037409
Chromosome Location	chr3:150582992-150582993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150558309..150558816-chr3:150582852..150583509,2	MCF-7	breast:
2	chr3:150505248..150506241-chr3:150582658..150583739,6	K562	blood:
3	chr3:150478755..150482911-chr3:150581723..150585653,5	MCF-7	breast:
4	chr3:150438851..150440084-chr3:150582767..150583714,6	MCF-7	breast:
5	chr3:150504367..150507442-chr3:150579602..150583163,3	MCF-7	breast:
6	chr3:150438822..150439787-chr3:150582598..150583745,7	K562	blood:
7	chr3:150548154..150548723-chr3:150582876..150583541,2	MCF-7	breast:
8	chr3:150482364..150486179-chr3:150581053..150584766,4	MCF-7	breast:
9	chr3:150505282..150506183-chr3:150582828..150583680,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000244265	Chromatin interaction
ENSG00000181788	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10513379	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12629256	0.88[EUR][1000 genomes]
rs1444198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1444199	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1444200	0.83[ASN][1000 genomes]
rs16862877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16862928	0.95[EUR][1000 genomes]
rs17283761	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2034158	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679986	0.88[ASN][1000 genomes]
rs4680004	0.92[ASN][1000 genomes]
rs4680006	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4680007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs56285716	0.93[ASN][1000 genomes]
rs56659353	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58091102	0.86[ASN][1000 genomes]
rs60107900	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60336215	0.81[EUR][1000 genomes]
rs60979559	0.82[EUR][1000 genomes]
rs61132047	0.86[EUR][1000 genomes]
rs62282691	0.89[ASN][1000 genomes]
rs67193230	0.95[EUR][1000 genomes]
rs6768276	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6775087	0.92[ASN][1000 genomes]
rs6781091	0.88[ASN][1000 genomes]
rs6783058	0.88[ASN][1000 genomes]
rs73152585	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv877646	chr3:150582992-150641304	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2037409	TM4SF4	cis	cerebellum	SCAN
rs2037409	TM4SF4	cis	parietal	SCAN
rs2037409	UBQLN4	cis	parietal	SCAN
rs2037409	PAPSS2	trans	lymphoblastoid	seeQTL
rs2037409	FAM194A	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150579600-150583000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr3:150580000-150584400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:150580600-150583000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:150582600-150583400	Enhancers	Placenta	Placenta
5	chr3:150582600-150583600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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