Variant report

Variant	rs883562
Chromosome Location	chr12:123460719-123460720
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFE2	chr12:123460441-123460811	K562	blood:	n/a	chr12:123460612-123460627
2	POLR2A	chr12:123458867-123460943	K562	blood:	n/a	n/a
3	STAT5A	chr12:123460311-123460834	K562	blood:	n/a	n/a
4	POLR2A	chr12:123458534-123466263	K562	blood:	n/a	n/a
5	POLR2A	chr12:123458857-123460826	K562	blood:	n/a	n/a
6	POLR2A	chr12:123460335-123460868	K562	blood:	n/a	n/a
7	POLR2A	chr12:123458680-123461169	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr12:123458851-123461232	K562	blood:	n/a	n/a
9	POLR2A	chr12:123460715-123460763	MCF10A-Er-Src	breast:	n/a	n/a
10	NR2F2	chr12:123460235-123460732	K562	blood:	n/a	n/a
11	POLR2A	chr12:123458643-123461407	HL-60	blood:	n/a	n/a
12	POLR2A	chr12:123458841-123461033	Raji	blood:	n/a	n/a
13	POLR2A	chr12:123458749-123460911	PBDE	blood:	n/a	n/a
14	MYC	chr12:123458710-123460779	K562	blood:	n/a	n/a
15	CUX1	chr12:123460224-123460931	K562	blood:	n/a	n/a
16	MXI1	chr12:123458420-123460816	IMR90	lung:	n/a	n/a
17	SIN3AK20	chr12:123459505-123460741	K562	blood:	n/a	n/a
18	POLR2A	chr12:123458857-123460868	ProgFib	skin:	n/a	n/a
19	TAF1	chr12:123459003-123460755	K562	blood:	n/a	n/a
20	ZC3H11A	chr12:123460470-123460791	K562	blood:	n/a	n/a
21	MTA3	chr12:123458461-123460859	GM12878	blood:	n/a	n/a
22	CBX3	chr12:123460186-123460798	K562	blood:	n/a	n/a
23	TBP	chr12:123458809-123460880	K562	blood:	n/a	n/a
24	EP300	chr12:123460508-123460723	GM12878	blood:	n/a	n/a
25	BHLHE40	chr12:123458658-123460887	K562	blood:	n/a	n/a
26	TAL1	chr12:123460371-123460815	K562	blood:	n/a	n/a
27	NR2F2	chr12:123458793-123460860	K562	blood:	n/a	n/a
28	BACH1	chr12:123460498-123460756	K562	blood:	n/a	n/a
29	POLR2A	chr12:123458875-123460947	K562	blood:	n/a	n/a
30	SIN3A	chr12:123458774-123460834	H1-hESC	embryonic stem cell:	n/a	chr12:123459190-123459201 chr12:123460430-123460443 chr12:123460436-123460444
31	GATA1	chr12:123458879-123460996	PBDE	blood:	n/a	n/a
32	MAX	chr12:123460480-123460757	K562	blood:	n/a	n/a
33	PML	chr12:123460435-123460861	K562	blood:	n/a	n/a
34	TEAD4	chr12:123458672-123461113	K562	blood:	n/a	n/a
35	POLR2A	chr12:123460287-123466106	K562	blood:	n/a	n/a
36	JUND	chr12:123460478-123460801	K562	blood:	n/a	chr12:123460542-123460551
37	ZMIZ1	chr12:123460417-123460742	K562	blood:	n/a	n/a
38	MYC	chr12:123458950-123460830	K562	blood:	n/a	n/a
39	POLR2A	chr12:123458704-123461070	GM12891	blood:	n/a	n/a
40	TAF1	chr12:123460268-123460828	K562	blood:	n/a	n/a
41	POLR2A	chr12:123458554-123460986	PFSK-1	brain:	n/a	n/a
42	YY1	chr12:123460294-123460752	K562	blood:	n/a	chr12:123460421-123460432
43	MAFF	chr12:123460327-123460811	K562	blood:	n/a	n/a
44	MYC	chr12:123458878-123460803	K562	blood:	n/a	n/a
45	POLR2A	chr12:123458693-123461033	HUVEC	blood vessel:	n/a	n/a
46	TBL1XR1	chr12:123460350-123460817	K562	blood:	n/a	n/a
47	HEY1	chr12:123460215-123460793	K562	blood:	n/a	n/a
48	POLR2A	chr12:123458558-123461092	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr12:123458870-123460940	K562	blood:	n/a	n/a
50	POLR2A	chr12:123458715-123460752	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123459054..123462367-chr12:123715409..123720380,5	K562	blood:
2	chr12:123458067..123461017-chr12:123715728..123717607,2	MCF-7	breast:
3	chr12:123458147..123462549-chr12:123715608..123720287,8	MCF-7	breast:
4	chr12:123444682..123447187-chr12:123459178..123461063,2	K562	blood:
5	chr12:120728398..120730404-chr12:123459731..123462257,2	MCF-7	breast:
6	chr12:123433587..123436454-chr12:123458977..123461529,2	K562	blood:
7	chr12:123344929..123347895-chr12:123458197..123461633,3	MCF-7	breast:
8	chr12:123344672..123346333-chr12:123459122..123461016,2	MCF-7	breast:
9	chr12:123457894..123461734-chr12:123715409..123718960,7	K562	blood:
10	chr12:123353599..123356535-chr12:123459324..123461652,2	MCF-7	breast:

No data

Variant related genes	Relation type
ARL6IP4	TF binding region
ABCB9	TF binding region
OGFOD2	TF binding region
ENSG00000139722	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10773921	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11060853	0.84[ASN][1000 genomes]
rs11608811	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11613937	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12425009	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425850	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1984658	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28755851	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741530	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3897102	0.98[ASN][1000 genomes]
rs4148862	0.80[EUR][1000 genomes]
rs4148863	0.80[EUR][1000 genomes]
rs4148866	0.83[ASN][1000 genomes]
rs4275659	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55742290	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61955196	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61955214	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7135296	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7296418	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305511	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7957096	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs884956	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv899578	chr12:123459005-123474529	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs883562	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs883562	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs883562	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs883562	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs883562	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs883562	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123458400-123460800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:123458400-123460800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:123458400-123460800	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:123458400-123461200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:123458600-123460800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:123458600-123461000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr12:123458600-123461000	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr12:123458800-123460800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:123459800-123461000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr12:123459800-123461400	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr12:123459800-123461400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:123459800-123461600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
13	chr12:123460000-123460800	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr12:123460000-123460800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:123460000-123460800	Flanking Active TSS	Fetal Brain Female	brain
16	chr12:123460000-123461000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr12:123460000-123461000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr12:123460000-123461000	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr12:123460000-123461000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr12:123460000-123461400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:123460000-123461400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:123460000-123461400	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr12:123460000-123461400	Flanking Active TSS	Liver	Liver
24	chr12:123460200-123460800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:123460200-123460800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr12:123460200-123460800	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr12:123460200-123460800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr12:123460200-123460800	Flanking Active TSS	Placenta	Placenta
29	chr12:123460200-123460800	Flanking Active TSS	Fetal Stomach	stomach
30	chr12:123460200-123460800	Flanking Active TSS	Right Ventricle	heart
31	chr12:123460200-123460800	Flanking Active TSS	Spleen	Spleen
32	chr12:123460200-123460800	Flanking Active TSS	NH-A	brain
33	chr12:123460200-123461000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr12:123460200-123461000	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr12:123460200-123461000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:123460200-123461000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr12:123460200-123461000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr12:123460200-123461000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr12:123460200-123461000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:123460200-123461000	Flanking Active TSS	Esophagus	oesophagus
41	chr12:123460200-123461000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr12:123460200-123461000	Flanking Active TSS	Fetal Muscle Trunk	muscle
43	chr12:123460200-123461000	Flanking Active TSS	Fetal Thymus	thymus
44	chr12:123460200-123461000	Flanking Active TSS	Thymus	Thymus
45	chr12:123460200-123461000	Flanking Active TSS	HUVEC	blood vessel
46	chr12:123460200-123461200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:123460200-123461200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:123460200-123461200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:123460200-123461200	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr12:123460200-123461200	Flanking Active TSS	Brain Hippocampus Middle	brain

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