Variant report

Variant	rs749279
Chromosome Location	chr14:97374262-97374263
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:97318739..97321684-chr14:97372950..97375820,2	K562	blood:

Variant related genes	Relation type
ENSG00000100749	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10145383	1.00[CHB][hapmap]
rs10146571	1.00[CHB][hapmap]
rs11160369	0.82[CHB][hapmap]
rs11160377	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627455	1.00[ASN][1000 genomes]
rs11628733	0.82[CHB][hapmap]
rs12101203	0.92[ASN][1000 genomes]
rs12433112	0.90[CHB][hapmap]
rs12434466	0.80[CHB][hapmap]
rs12586511	0.92[ASN][1000 genomes]
rs12589919	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12590169	0.92[ASN][1000 genomes]
rs12878184	0.90[CHB][hapmap]
rs12881995	0.87[ASN][1000 genomes]
rs12882038	0.93[ASN][1000 genomes]
rs12882853	1.00[CHB][hapmap]
rs12887093	0.87[ASN][1000 genomes]
rs12889255	0.92[ASN][1000 genomes]
rs12892609	0.92[ASN][1000 genomes]
rs12893513	0.93[ASN][1000 genomes]
rs12893711	0.93[ASN][1000 genomes]
rs12894533	0.87[ASN][1000 genomes]
rs12894621	0.90[CHB][hapmap]
rs12897588	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17191471	1.00[JPT][hapmap]
rs2145635	0.92[ASN][1000 genomes]
rs2145636	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs2180897	0.92[ASN][1000 genomes]
rs2224442	0.82[CHB][hapmap]
rs2224443	0.95[ASN][1000 genomes]
rs2230532	0.90[CHB][hapmap]
rs4270096	0.90[CHB][hapmap]
rs4900346	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4900348	0.89[ASN][1000 genomes]
rs4900350	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs4900351	1.00[CHB][hapmap]
rs4900352	0.93[ASN][1000 genomes]
rs4900353	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4905548	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4905549	0.92[ASN][1000 genomes]
rs4905550	0.92[ASN][1000 genomes]
rs4905551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4905558	0.90[CHB][hapmap]
rs4905561	0.95[ASN][1000 genomes]
rs4905562	0.82[ASN][1000 genomes]
rs4905563	0.82[ASN][1000 genomes]
rs4905567	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156355	0.90[CHB][hapmap]
rs7158545	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs723810	0.90[CHB][hapmap]
rs736929	1.00[CHB][hapmap]
rs764300	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8013081	0.90[CHB][hapmap]
rs8022152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323955	0.90[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044202	chr14:97155291-97683983	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv542179	chr14:97155291-97683983	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv948620	chr14:97334444-98133191	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv832867	chr14:97365919-97541763	Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs749279	VRK1	cis	cerebellum	SCAN
rs749279	C14orf177	cis	cerebellum	SCAN
rs749279	CLMN	cis	parietal	SCAN
rs749279	VRK1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:97331000-97378400	Weak transcription	A549	lung
2	chr14:97349200-97377400	Weak transcription	Primary T cells from cord blood	blood
3	chr14:97356000-97376600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr14:97362600-97374800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr14:97368600-97391400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:97368800-97374800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr14:97373000-97374800	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr14:97373000-97376000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr14:97373600-97375800	Weak transcription	K562	blood
10	chr14:97374000-97374400	Weak transcription	Primary B cells from cord blood	blood
11	chr14:97374000-97376600	ZNF genes & repeats	Dnd41	blood
12	chr14:97374200-97374600	Weak transcription	Primary monocytes fromperipheralblood	blood

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