Variant report

Variant	rs3811349
Chromosome Location	chr16:69791266-69791267
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:69791165-69791293	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:69790749-69791413	GM12892	blood:	n/a	n/a
3	POLR2A	chr16:69790852-69791573	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:69785030..69792317-chr16:69794435..69797821,11	MCF-7	breast:
2	chr16:69787301..69791461-chr16:69794716..69798365,9	K562	blood:
3	chr16:69362606..69365280-chr16:69790228..69792160,2	MCF-7	breast:
4	chr16:69756628..69762611-chr16:69781362..69792848,24	MCF-7	breast:

Variant related genes	Relation type
NOB1	TF binding region
WWP2	TF binding region
ENSG00000198373	Chromatin interaction
ENSG00000258429	Chromatin interaction
ENSG00000181019	Chromatin interaction
ENSG00000262136	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11075733	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11075734	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1139178	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11641521	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11643926	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11644838	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11644914	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12446201	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12596679	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12925371	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4078387	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4464069	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4497676	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4580150	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985518	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985523	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55701476	0.80[EUR][1000 genomes]
rs55863174	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55992518	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56282083	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57518557	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59295369	0.86[ASN][1000 genomes]
rs60231938	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61426398	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6499253	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6499255	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7189424	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73579458	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73579497	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8045682	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8059345	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[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	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3811349	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69789000-69795800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:69789200-69794600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr16:69789200-69795000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr16:69789200-69795000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr16:69789200-69795200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr16:69789200-69795400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr16:69789200-69795400	Weak transcription	GM12878-XiMat	blood
8	chr16:69789200-69795400	Weak transcription	HUVEC	blood vessel
9	chr16:69789200-69795600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:69789200-69795600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr16:69789200-69795600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr16:69789200-69795600	Weak transcription	Right Atrium	heart
13	chr16:69789200-69795600	Weak transcription	Osteobl	bone
14	chr16:69789200-69795800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr16:69789400-69795000	Weak transcription	Dnd41	blood
16	chr16:69789400-69795400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr16:69789400-69795600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr16:69789400-69795600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr16:69789400-69795600	Weak transcription	NHEK	skin
20	chr16:69789600-69795600	Weak transcription	A549	lung
21	chr16:69790000-69792400	Weak transcription	HepG2	liver
22	chr16:69791000-69791400	Enhancers	K562	blood
23	chr16:69791200-69791400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr16:69791200-69791600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links