Variant report

Variant	rs7312062
Chromosome Location	chr12:4715082-4715083
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	POLR2A	chr12:4714783-4715082	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr12:4714834-4715312	MCF10A-Er-Src	breast:	n/a	n/a
3	MXI1	chr12:4713666-4715111	SK-N-SH	brain:	n/a	n/a
4	STAT3	chr12:4715052-4715432	MCF10A-Er-Src	breast:	n/a	chr12:4715240-4715251
5	FOS	chr12:4715061-4715402	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr12:4714973-4715414	MCF10A-Er-Src	breast:	n/a	chr12:4715240-4715251
7	STAT1	chr12:4714908-4715628	Hela-S3	cervix:	n/a	n/a
8	FOS	chr12:4715023-4715359	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr12:4714962-4715408	HUVEC	blood vessel:	n/a	n/a
10	FOS	chr12:4714991-4715401	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr12:4714953-4715627	MCF10A-Er-Src	breast:	n/a	chr12:4715240-4715251

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

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

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10444481	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10774249	0.85[CEU][hapmap]
rs10774252	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10774253	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10774254	0.86[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849105	0.82[TSI][hapmap]
rs10849109	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849110	0.94[ASN][1000 genomes]
rs10849112	0.86[TSI][hapmap]
rs11063261	0.86[CEU][hapmap];0.86[TSI][hapmap]
rs11063267	0.86[ASN][1000 genomes]
rs11063270	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12227238	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12298137	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12366671	0.86[CEU][hapmap];0.86[TSI][hapmap]
rs1860342	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1990316	0.86[TSI][hapmap]
rs2011298	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072355	0.93[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2072356	0.93[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2267544	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2267547	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299834	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4147675	0.80[CEU][hapmap];0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs6416316	0.86[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs7133467	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7133999	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs7300882	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7301072	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7310920	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7310971	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7311845	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs758532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs917565	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs917566	0.92[EUR][1000 genomes]
rs979878	0.86[TSI][hapmap]
rs997373	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv898617	chr12:4715082-4768619	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7312062	DYRK4	Cis_1M	lymphoblastoid	RTeQTL
rs7312062	AKAP3	cis	multi-tissue	Pritchard
rs7312062	DYRK4	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4713800-4715200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:4713800-4715200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr12:4713800-4715200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:4713800-4715200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:4713800-4715200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:4713800-4715200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:4713800-4715200	Active TSS	K562	blood
8	chr12:4713800-4715400	Active TSS	HMEC	breast
9	chr12:4713800-4715400	Active TSS	NHLF	lung
10	chr12:4714000-4715200	Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr12:4714000-4715200	Active TSS	Ovary	ovary
12	chr12:4714000-4715200	Active TSS	Rectal Mucosa Donor 31	rectum
13	chr12:4714000-4715200	Active TSS	GM12878-XiMat	blood
14	chr12:4714200-4715200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:4714400-4715200	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr12:4714400-4715200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:4714400-4715200	Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr12:4714400-4715200	Flanking Active TSS	Dnd41	blood
19	chr12:4714400-4715800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:4714400-4715800	Weak transcription	Gastric	stomach
21	chr12:4714400-4715800	Weak transcription	Pancreas	Pancrea
22	chr12:4714400-4715800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:4714400-4716200	Weak transcription	Stomach Mucosa	stomach
24	chr12:4714400-4716400	Weak transcription	Lung	lung
25	chr12:4714400-4719400	Weak transcription	Spleen	Spleen
26	chr12:4714400-4722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:4714400-4724800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:4714400-4726400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:4714600-4715200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr12:4714600-4715200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr12:4714600-4715200	Enhancers	Fetal Heart	heart
32	chr12:4714600-4715200	Enhancers	Thymus	Thymus
33	chr12:4714600-4715400	Flanking Active TSS	HUVEC	blood vessel
34	chr12:4714600-4715800	Weak transcription	Left Ventricle	heart
35	chr12:4714600-4716000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:4714600-4716200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:4714600-4716200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:4714600-4718400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr12:4714600-4718600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:4714600-4719200	Weak transcription	Aorta	Aorta
41	chr12:4714600-4719200	Weak transcription	Placenta	Placenta
42	chr12:4714600-4719800	Weak transcription	Psoas Muscle	Psoas
43	chr12:4714600-4721600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:4714600-4721800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:4714600-4721800	Weak transcription	Brain Germinal Matrix	brain
46	chr12:4714600-4721800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr12:4714600-4722200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:4714600-4725400	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:4714600-4726200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:4714600-4726800	Weak transcription	Right Ventricle	heart

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