Variant report

Variant	rs1112543
Chromosome Location	chr1:113931805-113931806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr1:113930554-113933084	HEK293	kidney:	n/a	n/a
2	MYBL2	chr1:113931117-113931817	HepG2	liver:	n/a	n/a
3	GATA1	chr1:113930839-113931840	PBDE	blood:	n/a	n/a
4	GATA3	chr1:113930714-113931911	SK-N-SH	brain:	n/a	n/a
5	SP1	chr1:113931156-113931879	A549	lung:	n/a	n/a
6	GATA2	chr1:113930773-113931818	SH-SY5Y	brain:	n/a	n/a
7	EP300	chr1:113931121-113931831	A549	lung:	n/a	n/a
8	MAX	chr1:113931045-113931817	MCF-7	breast:	n/a	n/a
9	NR2F2	chr1:113930853-113931864	MCF-7	breast:	n/a	n/a
10	KAP1	chr1:113930717-113932926	U2OS	brain:	n/a	n/a
11	POLR2A	chr1:113931297-113933512	MCF-7	breast:	n/a	n/a
12	SIN3AK20	chr1:113931026-113931905	MCF-7	breast:	n/a	n/a
13	MAX	chr1:113931176-113931831	HepG2	liver:	n/a	n/a
14	GATA3	chr1:113930685-113931872	MCF-7	breast:	n/a	n/a
15	SMARCC1	chr1:113931771-113932861	Hela-S3	cervix:	n/a	n/a
16	NR2F2	chr1:113930993-113931850	MCF-7	breast:	n/a	n/a
17	FOXA2	chr1:113930941-113932142	HepG2	liver:	n/a	n/a
18	TCF12	chr1:113931002-113931826	A549	lung:	n/a	n/a
19	SIN3A	chr1:113931674-113934672	H1-hESC	embryonic stem cell:	n/a	chr1:113933176-113933184 chr1:113933431-113933442
20	MXI1	chr1:113930460-113936450	SK-N-SH	brain:	n/a	n/a
21	TCF12	chr1:113930739-113931861	SK-N-SH	brain:	n/a	n/a
22	GATA3	chr1:113930854-113931979	MCF-7	breast:	n/a	n/a
23	SIN3AK20	chr1:113930653-113931978	MCF-7	breast:	n/a	n/a
24	EP300	chr1:113930516-113935379	SK-N-SH	brain:	n/a	chr1:113935085-113935099
25	SP1	chr1:113931581-113932000	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113929860..113932778-chr17:56735135..56736789,2	MCF-7	breast:
2	chr1:113927002..113929717-chr1:113930255..113932026,2	MCF-7	breast:
3	chr1:113931751..113937304-chr1:113991927..113997733,10	MCF-7	breast:
4	chr1:113804322..113806527-chr1:113931501..113933105,2	MCF-7	breast:
5	chr1:113775818..113778014-chr1:113929925..113932483,2	MCF-7	breast:
6	chr1:113931119..113932828-chr1:113952487..113954122,2	K562	blood:
7	chr1:113820435..113822948-chr1:113930642..113932953,2	MCF-7	breast:
8	chr1:113822173..113823702-chr1:113930402..113933274,2	MCF-7	breast:
9	chr1:113930334..113933089-chr1:114124806..114127254,2	MCF-7	breast:
10	chr1:113751160..113752973-chr1:113930438..113931950,2	MCF-7	breast:
11	chr1:113930366..113932771-chr1:114217459..114219362,2	MCF-7	breast:

No data

Variant related genes	Relation type
MAGI3	TF binding region
ENSG00000232499	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10458458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10458459	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10857994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11102627	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[ASN][1000 genomes]
rs11102628	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[ASN][1000 genomes]
rs11102630	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11102636	0.80[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs11102637	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs11102638	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs11102639	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs11102641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11102647	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs1112085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12021783	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12022213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs12022849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs12023641	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12024139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs12024428	0.93[ASN][1000 genomes]
rs12026682	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs12029305	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12030900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12032395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12034178	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12038473	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs12038879	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12039603	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12039669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12039944	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs12044485	0.80[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12045148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12045559	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12046451	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12048327	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12049093	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12049447	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12567622	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568854	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1418607	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1539411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1573996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap]
rs1936927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs1936928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2027536	0.94[ASN][1000 genomes]
rs2027537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4838987	0.82[AMR][1000 genomes]
rs4838988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap]
rs4839320	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[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4839323	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs4839324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs55737954	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66565865	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6688827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[ASN][1000 genomes]
rs72687924	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9787276	0.93[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	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1112543	CAPZA1	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113931000-113932000	Enhancers	K562	blood
2	chr1:113931200-113932000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:113931200-113932000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:113931200-113932000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr1:113931200-113932000	Enhancers	Brain Angular Gyrus	brain
6	chr1:113931200-113932400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr1:113931200-113932400	Flanking Active TSS	HMEC	breast
8	chr1:113931200-113932400	Flanking Active TSS	NHEK	skin
9	chr1:113931200-113932600	Flanking Active TSS	Osteobl	bone
10	chr1:113931200-113934400	Active TSS	Rectal Smooth Muscle	rectum
11	chr1:113931200-113935600	Active TSS	NHDF-Ad	bronchial
12	chr1:113931200-113937200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:113931400-113932000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
14	chr1:113931400-113932000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:113931400-113932000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:113931400-113932000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:113931400-113932000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:113931400-113932000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:113931400-113932000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:113931400-113932000	Enhancers	Brain Hippocampus Middle	brain
21	chr1:113931400-113932000	Enhancers	Brain Substantia Nigra	brain
22	chr1:113931400-113932000	Enhancers	Fetal Muscle Leg	muscle
23	chr1:113931400-113932000	Bivalent Enhancer	Fetal Thymus	thymus
24	chr1:113931400-113932200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:113931400-113932200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:113931400-113932200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr1:113931400-113932200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:113931400-113932400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:113931400-113932400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:113931400-113932400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:113931400-113932400	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr1:113931400-113932400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr1:113931400-113932400	Flanking Active TSS	Hela-S3	cervix
34	chr1:113931400-113932400	Flanking Active TSS	HSMM	muscle
35	chr1:113931400-113932600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:113931400-113932600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:113931400-113932600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr1:113931400-113932600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:113931400-113932600	Flanking Active TSS	Liver	Liver
40	chr1:113931400-113932600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr1:113931400-113932600	Flanking Active TSS	HUVEC	blood vessel
42	chr1:113931400-113932800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:113931400-113933200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:113931400-113934400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr1:113931400-113934800	Active TSS	Gastric	stomach
46	chr1:113931400-113934800	Active TSS	Left Ventricle	heart
47	chr1:113931400-113934800	Active TSS	Pancreas	Pancrea
48	chr1:113931400-113935000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:113931400-113935000	Active TSS	A549	lung
50	chr1:113931600-113932000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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