Variant report

Variant	rs2286576
Chromosome Location	chr12:4714008-4714009
allele	A/C
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	CTCF	chr12:4713960-4714110	GM12801	blood:	n/a	chr12:4713977-4713990
2	POLR2A	chr12:4713918-4714353	GM12891	blood:	n/a	n/a
3	RCOR1	chr12:4713802-4714255	K562	blood:	n/a	n/a
4	E2F6	chr12:4713917-4714254	K562	blood:	n/a	n/a
5	CTCF	chr12:4713844-4714340	MCF-7	breast:	n/a	chr12:4713977-4713990
6	POLR2A	chr12:4713861-4714421	U87	brain:	n/a	n/a
7	CTCF	chr12:4713920-4714070	HRPEpiC	eye:	n/a	chr12:4713977-4713990
8	CTCF	chr12:4713819-4714139	HUVEC	blood vessel:	n/a	chr12:4713977-4713990
9	CTCF	chr12:4713920-4714070	AG10803	skin:	n/a	chr12:4713977-4713990
10	MXI1	chr12:4713895-4714398	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr12:4713920-4714070	GM12872	blood:	n/a	chr12:4713977-4713990
12	POLR2A	chr12:4713856-4714336	SK-N-SH	brain:	n/a	n/a
13	TAF1	chr12:4713981-4714266	SK-N-SH	brain:	n/a	n/a
14	RAD21	chr12:4713809-4714300	ECC-1	luminal epithelium:	n/a	n/a
15	CTCF	chr12:4713920-4714070	HepG2	liver:	n/a	chr12:4713977-4713990
16	MAX	chr12:4713755-4714364	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:4713964-4714334	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZNF143	chr12:4713786-4714219	H1-hESC	embryonic stem cell:	n/a	n/a
19	CHD2	chr12:4713886-4714287	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:4713916-4714298	PANC-1	pancreas:	n/a	n/a
21	CTCF	chr12:4713940-4714090	GM12869	blood:	n/a	chr12:4713977-4713990
22	POLR2A	chr12:4713914-4714352	HepG2	liver:	n/a	n/a
23	SIN3AK20	chr12:4713843-4714264	SK-N-SH	brain:	n/a	n/a
24	HDAC2	chr12:4713859-4714203	HepG2	liver:	n/a	n/a
25	BACH1	chr12:4713891-4714091	K562	blood:	n/a	n/a
26	POLR2A	chr12:4713847-4714339	MCF10A-Er-Src	breast:	n/a	n/a
27	CTCF	chr12:4713960-4714110	HAc	cerebellar:	n/a	chr12:4713977-4713990
28	POLR2A	chr12:4713779-4714504	SK-N-MC	brain:	n/a	n/a
29	MAX	chr12:4713816-4714395	K562	blood:	n/a	n/a
30	CREB1	chr12:4713721-4714403	HepG2	liver:	n/a	n/a
31	CTCF	chr12:4713920-4714070	GM12870	blood:	n/a	chr12:4713977-4713990
32	CTCF	chr12:4713960-4714110	A549	lung:	n/a	chr12:4713977-4713990
33	CTCF	chr12:4713900-4714050	HepG2	liver:	n/a	chr12:4713977-4713990
34	CTCF	chr12:4713760-4714193	HepG2	liver:	n/a	chr12:4713977-4713990
35	YY1	chr12:4713790-4714463	ECC-1	luminal epithelium:	n/a	n/a
36	CTCF	chr12:4713920-4714070	WERI-Rb-1	eye:	n/a	chr12:4713977-4713990
37	SIN3A	chr12:4713833-4714455	H1-hESC	embryonic stem cell:	n/a	n/a
38	RAD21	chr12:4713777-4714297	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr12:4713900-4714050	AG04449	skin:	n/a	chr12:4713977-4713990
40	CTCF	chr12:4713828-4714190	ProgFib	skin:	n/a	chr12:4713977-4713990
41	CREB1	chr12:4713831-4714405	GM12878	blood:	n/a	n/a
42	CREB1	chr12:4713850-4714330	A549	lung:	n/a	n/a
43	USF2	chr12:4713851-4714252	GM12878	blood:	n/a	n/a
44	POU2F2	chr12:4713756-4714374	GM12878	blood:	n/a	chr12:4713894-4713906
45	CTCF	chr12:4713900-4714050	GM12873	blood:	n/a	chr12:4713977-4713990
46	TBL1XR1	chr12:4713821-4714218	GM12878	blood:	n/a	n/a
47	CTCF	chr12:4713920-4714070	K562	blood:	n/a	chr12:4713977-4713990
48	JUND	chr12:4713825-4714396	A549	lung:	n/a	n/a
49	POLR2A	chr12:4713923-4714290	GM12878	blood:	n/a	n/a
50	CTCF	chr12:4713900-4714050	GM12864	blood:	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
ENSG00000272921	TF binding region
ENSG00000256748	TF binding region
ENSG00000010219	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1008578	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs10744653	0.90[GIH][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs10744654	0.83[EUR][1000 genomes]
rs10774245	0.90[EUR][1000 genomes]
rs11063253	0.88[GIH][hapmap];0.91[TSI][hapmap]
rs12303320	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12313377	0.81[EUR][1000 genomes]
rs12828416	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1860343	0.89[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1860344	0.88[EUR][1000 genomes]
rs1974602	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2299833	0.81[EUR][1000 genomes]
rs2302248	0.90[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2884671	0.82[EUR][1000 genomes]
rs35131771	0.83[EUR][1000 genomes]
rs7136668	0.82[CEU][hapmap];0.90[GIH][hapmap]
rs7300543	0.90[GIH][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs730065	0.90[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs7305150	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs7972737	0.85[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs7975484	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs7977981	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2286576	DYRK4	Cis_1M	lymphoblastoid	RTeQTL
rs2286576	AKAP3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4713600-4714600	Active TSS	Brain Anterior Caudate	brain
2	chr12:4713600-4714800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr12:4713600-4714800	Active TSS	Fetal Kidney	kidney
4	chr12:4713600-4715000	Active TSS	HSMM	muscle
5	chr12:4713800-4714200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:4713800-4714200	Active TSS	Primary B cells from cord blood	blood
7	chr12:4713800-4714200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr12:4713800-4714200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:4713800-4714200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:4713800-4714400	Active TSS	Primary T cells from cord blood	blood
11	chr12:4713800-4714400	Active TSS	Primary hematopoietic stem cells	blood
12	chr12:4713800-4714400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:4713800-4714400	Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr12:4713800-4714400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:4713800-4714400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:4713800-4714400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
17	chr12:4713800-4714600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr12:4713800-4714600	Active TSS	Primary monocytes fromperipheralblood	blood
19	chr12:4713800-4714600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr12:4713800-4714600	Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr12:4713800-4714600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr12:4713800-4714600	Active TSS	Aorta	Aorta
23	chr12:4713800-4714600	Active TSS	Brain Germinal Matrix	brain
24	chr12:4713800-4714600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr12:4713800-4714600	Active TSS	Fetal Brain Female	brain
26	chr12:4713800-4714600	Active TSS	Thymus	Thymus
27	chr12:4713800-4714600	Active TSS	Monocytes-CD14+_RO01746	blood
28	chr12:4713800-4714800	Active TSS	H1 Cell Line	embryonic stem cell
29	chr12:4713800-4714800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:4713800-4714800	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:4713800-4714800	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:4713800-4714800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:4713800-4714800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:4713800-4714800	Active TSS	Brain Substantia Nigra	brain
35	chr12:4713800-4714800	Active TSS	Fetal Lung	lung
36	chr12:4713800-4714800	Active TSS	Fetal Thymus	thymus
37	chr12:4713800-4714800	Active TSS	Stomach Smooth Muscle	stomach
38	chr12:4713800-4714800	Active TSS	HSMMtube	muscle
39	chr12:4713800-4715000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:4713800-4715000	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr12:4713800-4715000	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:4713800-4715000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:4713800-4715000	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr12:4713800-4715000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:4713800-4715000	Active TSS	Muscle Satellite Cultured Cells	--
46	chr12:4713800-4715000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:4713800-4715000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:4713800-4715000	Active TSS	Brain Angular Gyrus	brain
49	chr12:4713800-4715000	Active TSS	Brain Hippocampus Middle	brain
50	chr12:4713800-4715000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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