Variant report

Variant	rs1860343
Chromosome Location	chr12:4713709-4713710
allele	A/G
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	MXI1	chr12:4713666-4715111	SK-N-SH	brain:	n/a	n/a
2	E2F6	chr12:4713687-4714510	A549	lung:	n/a	n/a
3	RAD21	chr12:4713543-4714587	SK-N-SH	brain:	n/a	n/a
4	SPI1	chr12:4713683-4714311	HL-60	blood:	n/a	chr12:4713963-4713976
5	ZNF384	chr12:4713648-4714186	K562	blood:	n/a	n/a
6	MXI1	chr12:4713654-4714793	IMR90	lung:	n/a	n/a
7	MAZ	chr12:4713533-4714501	IMR90	lung:	n/a	n/a
8	KAP1	chr12:4713674-4714481	HEK293	kidney:	n/a	chr12:4714055-4714063
9	MAX	chr12:4713706-4714504	A549	lung:	n/a	n/a
10	CEBPB	chr12:4713688-4714238	A549	lung:	n/a	n/a
11	HCFC1	chr12:4713602-4714699	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr12:4713437-4714437	SK-N-SH	brain:	n/a	chr12:4713977-4713990
13	CTCF	chr12:4713545-4714711	A549	lung:	n/a	chr12:4713977-4713990

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4712076..4715630-chr12:4717272..4720188,3	K562	blood:
2	chr12:4712752..4714423-chr12:4719213..4721715,2	K562	blood:

Variant related genes	Relation type
DYRK4	TF binding region
ENSG00000256748	TF binding region
ENSG00000272921	TF binding region
ENSG00000010219	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1008578	0.96[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10744653	0.89[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10744654	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10774245	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11063253	0.85[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs11063280	0.84[ASN][1000 genomes]
rs11063282	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs11063285	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs12303320	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12308883	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs12310639	0.94[ASN][1000 genomes]
rs12313377	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12318966	0.83[ASN][1000 genomes]
rs12811453	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs12828416	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12829711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16931616	0.83[ASN][1000 genomes]
rs16931620	0.83[ASN][1000 genomes]
rs1860344	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1974602	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1990311	0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs2041293	0.86[EUR][1000 genomes]
rs2267548	0.83[ASN][1000 genomes]
rs2286576	0.89[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2299833	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2302246	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs2302248	0.89[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2884671	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35131771	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35167443	0.84[ASN][1000 genomes]
rs4147671	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs4147672	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs4147673	0.84[ASN][1000 genomes]
rs4147677	0.83[ASN][1000 genomes]
rs4147678	0.83[ASN][1000 genomes]
rs4147679	0.83[ASN][1000 genomes]
rs4147680	0.83[ASN][1000 genomes]
rs4147684	0.83[ASN][1000 genomes]
rs4147685	0.83[ASN][1000 genomes]
rs4766260	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs4766264	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4766267	0.91[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs4766269	0.83[ASN][1000 genomes]
rs61909965	0.83[ASN][1000 genomes]
rs7136668	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs720673	0.82[EUR][1000 genomes]
rs7300543	0.89[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs730065	0.89[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs7305150	0.96[CEU][hapmap];1.00[EUR][1000 genomes]
rs7312402	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs7958182	0.83[ASN][1000 genomes]
rs7972657	0.83[ASN][1000 genomes]
rs7972737	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972920	0.83[ASN][1000 genomes]
rs7975484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977981	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs876586	0.94[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	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer 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 miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1860343	DYRK4	Cis_1M	lymphoblastoid	RTeQTL
rs1860343	AKAP3	cis	parietal	SCAN
rs1860343	DYRK4	cis	multi-tissue	Pritchard
rs1860343	NOP2	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4709000-4713800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:4709400-4713800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:4713600-4713800	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr12:4713600-4713800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:4713600-4713800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr12:4713600-4713800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr12:4713600-4713800	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr12:4713600-4713800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr12:4713600-4713800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:4713600-4713800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr12:4713600-4713800	Enhancers	Brain Hippocampus Middle	brain
12	chr12:4713600-4713800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr12:4713600-4713800	Enhancers	Brain Substantia Nigra	brain
14	chr12:4713600-4713800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr12:4713600-4714000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:4713600-4714000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:4713600-4714000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr12:4713600-4714000	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr12:4713600-4714000	Flanking Active TSS	Dnd41	blood
20	chr12:4713600-4714600	Active TSS	Brain Anterior Caudate	brain
21	chr12:4713600-4714800	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr12:4713600-4714800	Active TSS	Fetal Kidney	kidney
23	chr12:4713600-4715000	Active TSS	HSMM	muscle

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