Variant report

Variant	rs560048
Chromosome Location	chr12:57829129-57829130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr12:57828162-57829137	HepG2	liver:	n/a	n/a
2	HEY1	chr12:57829108-57829365	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:57828119-57829450	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:57829012-57829447	NB4	blood:	n/a	n/a
5	HEY1	chr12:57828155-57829524	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:57829040-57829298	HepG2	liver:	n/a	n/a
7	MBD4	chr12:57828842-57829377	HepG2	liver:	n/a	n/a
8	ELF1	chr12:57829094-57829455	HepG2	liver:	n/a	n/a
9	ELF1	chr12:57829119-57829419	HepG2	liver:	n/a	n/a
10	ELF1	chr12:57829068-57829412	K562	blood:	n/a	n/a
11	POLR2A	chr12:57829052-57829388	HepG2	liver:	n/a	n/a
12	MYBL2	chr12:57828834-57829427	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:57828280-57829374	HepG2	liver:	n/a	n/a
14	RUNX3	chr12:57829055-57829432	GM12878	blood:	n/a	n/a
15	ELF1	chr12:57829073-57829390	GM12878	blood:	n/a	n/a
16	RUNX3	chr12:57829044-57829434	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:57829115-57829368	HepG2	liver:	n/a	n/a
18	FOXA1	chr12:57829118-57829527	HepG2	liver:	n/a	n/a
19	MAX	chr12:57829108-57829385	NB4	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57821945..57831494-chr12:57839441..57852842,32	K562	blood:
2	chr12:57822828..57827240-chr12:57828141..57836129,12	MCF-7	breast:

No data

Variant related genes	Relation type
R3HDM2	TF binding region
ENSG00000258001	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000179912	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10747777	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10747778	1.00[CEU][hapmap]
rs10783818	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs10783819	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10783823	0.80[ASN][1000 genomes]
rs10876976	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs10876977	0.82[EUR][1000 genomes]
rs10876978	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876980	0.82[EUR][1000 genomes]
rs10876981	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876983	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172156	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs11172169	0.89[CEU][hapmap]
rs11172170	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11172190	0.92[CEU][hapmap]
rs11172191	0.83[EUR][1000 genomes]
rs11172205	0.85[EUR][1000 genomes]
rs11172211	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11172214	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172222	0.89[EUR][1000 genomes]
rs11609986	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs12230111	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12296766	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs12310220	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs12423654	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12579911	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12812140	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs1284252	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1798710	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2063778	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2280139	0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28504983	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3923885	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.97[TSI][hapmap]
rs4075325	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs4108243	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4760228	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760236	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760244	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760305	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760306	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760308	1.00[CEU][hapmap]
rs4760348	1.00[CEU][hapmap]
rs481196	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs491750	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs492749	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs512223	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs533975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537482	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs543410	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568793	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs575153	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6581131	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs6581134	0.81[ASW][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap]
rs6581136	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs6581139	0.81[ASN][1000 genomes]
rs7132367	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7133939	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7135142	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs7298418	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs7303070	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7307059	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs7309659	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs7398058	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs7486863	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs7977908	1.00[CEU][hapmap]
rs7980310	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9738004	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs560048	KIAA0748	cis	cerebellum	SCAN
rs560048	SPRY2	trans	lymphoblastoid	seeQTL
rs560048	KIF5A	cis	cerebellum	SCAN
rs560048	TSPAN31	cis	cerebellum	SCAN
rs560048	SP7	cis	parietal	SCAN
rs560048	KRT81	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57825600-57848600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57826400-57829200	Weak transcription	Dnd41	blood
3	chr12:57828000-57829200	Enhancers	A549	lung
4	chr12:57828000-57829200	Flanking Active TSS	HepG2	liver
5	chr12:57828000-57829600	Enhancers	Fetal Intestine Small	intestine
6	chr12:57828000-57829600	Enhancers	Fetal Muscle Leg	muscle
7	chr12:57828200-57829400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr12:57828400-57829400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:57828400-57829600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr12:57828400-57829600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr12:57828400-57829600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:57828400-57829600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:57828400-57829600	Enhancers	Fetal Muscle Trunk	muscle
14	chr12:57828400-57829600	Enhancers	K562	blood
15	chr12:57828400-57829800	Enhancers	Fetal Stomach	stomach
16	chr12:57828400-57831800	Active TSS	Liver	Liver
17	chr12:57828600-57829400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:57828600-57829400	Enhancers	Pancreas	Pancrea
19	chr12:57828600-57829400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr12:57828600-57829600	Enhancers	Primary hematopoietic stem cells	blood
21	chr12:57828800-57829600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr12:57828800-57829600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr12:57828800-57829600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:57828800-57829600	Enhancers	Fetal Thymus	thymus

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