Variant report

Variant	rs12576058
Chromosome Location	chr11:72394706-72394707
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	chr11:72394395-72394912	HepG2	liver:	n/a	n/a
2	ZBTB7A	chr11:72394699-72395209	K562	blood:	n/a	chr11:72395023-72395032
3	CTCF	chr11:72394580-72394730	AG04449	skin:	n/a	n/a
4	RAD21	chr11:72394556-72395266	A549	lung:	n/a	chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395021-72395031 chr11:72394701-72394713
5	POLR2A	chr11:72394447-72395399	GM12892	blood:	n/a	n/a
6	RAD21	chr11:72394655-72395333	ECC-1	luminal epithelium:	n/a	chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395021-72395031 chr11:72394701-72394713
7	RAD21	chr11:72394546-72395211	MCF-7	breast:	n/a	chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395021-72395031 chr11:72394701-72394713
8	CTCF	chr11:72394522-72396150	HCT-116	colon:	n/a	chr11:72395750-72395759 chr11:72395020-72395030 chr11:72394724-72394732 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72394952-72394970 chr11:72394954-72394967 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
9	RAD21	chr11:72394555-72396153	SK-N-SH	brain:	n/a	chr11:72395633-72395643 chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395751-72395764 chr11:72395021-72395031 chr11:72395803-72395816 chr11:72394701-72394713 chr11:72395753-72395763 chr11:72395632-72395645
10	RAD21	chr11:72394613-72395238	MCF-7	breast:	n/a	chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395021-72395031 chr11:72394701-72394713
11	CTCF	chr11:72394627-72395365	K562	blood:	n/a	chr11:72395020-72395030 chr11:72394724-72394732 chr11:72394952-72394970 chr11:72394954-72394967
12	POLR2A	chr11:72388985-72396153	GM12892	blood:	n/a	n/a
13	POLR2A	chr11:72394596-72395114	GM12878	blood:	n/a	n/a
14	RAD21	chr11:72394682-72395230	A549	lung:	n/a	chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395021-72395031 chr11:72394701-72394713
15	CTCF	chr11:72394637-72394754	GM19240	blood:	n/a	chr11:72394724-72394732
16	CTCF	chr11:72394603-72394745	GM19239	blood:	n/a	chr11:72394724-72394732
17	POLR2A	chr11:72391409-72395319	GM12891	blood:	n/a	n/a
18	POLR2A	chr11:72394518-72395246	K562	blood:	n/a	n/a
19	SMC3	chr11:72394433-72395356	SK-N-SH	brain:	n/a	chr11:72394954-72394968 chr11:72394701-72394711 chr11:72395021-72395031
20	POLR2A	chr11:72393504-72395948	GM12878	blood:	n/a	n/a
21	POLR2A	chr11:72391380-72396040	HL-60	blood:	n/a	n/a
22	POLR2A	chr11:72388899-72396049	K562	blood:	n/a	n/a
23	POLR2A	chr11:72394643-72395051	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr11:72394576-72395205	K562	blood:	n/a	n/a
25	RAD21	chr11:72394698-72395166	H1-hESC	embryonic stem cell:	n/a	chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395021-72395031 chr11:72394701-72394713
26	CTCF	chr11:72394603-72395532	GM12891	blood:	n/a	chr11:72395020-72395030 chr11:72394724-72394732 chr11:72394952-72394970 chr11:72394954-72394967
27	SMC3	chr11:72394689-72395237	Hela-S3	cervix:	n/a	chr11:72394954-72394968 chr11:72394701-72394711 chr11:72395021-72395031
28	POLR2A	chr11:72394427-72395066	K562	blood:	n/a	n/a
29	PML	chr11:72394391-72395152	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:72389086-72395911	GM12892	blood:	n/a	n/a
31	FOXM1	chr11:72394684-72395350	GM12878	blood:	n/a	n/a
32	POLR2A	chr11:72394544-72394866	HepG2	liver:	n/a	n/a
33	POLR2A	chr11:72388792-72395937	GM12891	blood:	n/a	n/a
34	POLR2A	chr11:72388800-72396117	GM12878	blood:	n/a	n/a
35	POLR2A	chr11:72394639-72395509	GM12891	blood:	n/a	n/a
36	NFATC1	chr11:72394619-72395313	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:72391252-72395172	SK-N-MC	brain:	n/a	n/a
38	RAD21	chr11:72394605-72395219	H1-hESC	embryonic stem cell:	n/a	chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395021-72395031 chr11:72394701-72394713
39	POLR2A	chr11:72394517-72396053	GM12878	blood:	n/a	n/a
40	TBP	chr11:72394667-72395183	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr11:72394603-72396062	MCF-7	breast:	n/a	chr11:72395750-72395759 chr11:72395020-72395030 chr11:72394724-72394732 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72394952-72394970 chr11:72394954-72394967 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
42	ELF1	chr11:72394420-72395109	GM12878	blood:	n/a	chr11:72394755-72394768
43	MTA3	chr11:72394519-72395383	GM12878	blood:	n/a	n/a
44	ELF1	chr11:72394607-72394919	K562	blood:	n/a	chr11:72394755-72394768
45	POLR2A	chr11:72389164-72395995	GM12878	blood:	n/a	n/a
46	CTCF	chr11:72394276-72396282	A549	lung:	n/a	chr11:72395750-72395759 chr11:72395020-72395030 chr11:72394724-72394732 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72394952-72394970 chr11:72394954-72394967 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
47	CTCF	chr11:72394635-72394720	MCF-7	breast:	n/a	n/a
48	RAD21	chr11:72394563-72395365	HCT-116	colon:	n/a	chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395021-72395031 chr11:72394701-72394713
49	HCFC1	chr11:72394439-72396120	Hela-S3	cervix:	n/a	n/a
50	RAD21	chr11:72394523-72395307	HCT-116	colon:	n/a	chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395021-72395031 chr11:72394701-72394713

No.	Distal block	Cell Line	Cell type
1	chr11:72301882..72302760-chr11:72394504..72395418,2	MCF-7	breast:
2	chr11:72300586..72302823-chr11:72392503..72395440,2	MCF-7	breast:
3	chr11:72386808..72388323-chr11:72393446..72395639,2	K562	blood:
4	chr11:72309161..72310639-chr11:72394269..72395813,13	MCF-7	breast:
5	chr11:72296452..72297372-chr11:72394539..72395851,6	K562	blood:
6	chr11:71933813..71936010-chr11:72394188..72397078,2	MCF-7	breast:
7	chr11:72300511..72301381-chr11:72394523..72395807,4	MCF-7	breast:
8	chr11:72392980..72396012-chr11:72397929..72401582,3	K562	blood:
9	chr11:72193462..72193981-chr11:72394566..72395462,2	K562	blood:
10	chr11:72296491..72297510-chr11:72394098..72395409,7	MCF-7	breast:
11	chr11:72309760..72310559-chr11:72394464..72395426,5	K562	blood:
12	chr11:72390674..72393188-chr11:72394273..72396002,3	MCF-7	breast:
13	chr11:72394488..72395414-chr11:72889125..72889716,2	K562	blood:
14	chr11:72296372..72297374-chr11:72394518..72396001,14	MCF-7	breast:
15	chr11:72300497..72301443-chr11:72394476..72395408,5	K562	blood:
16	chr11:72384189..72387111-chr11:72392506..72394977,2	MCF-7	breast:

Variant related genes	Relation type
ARAP1-AS1	TF binding region
ENSG00000165458	Chromatin interaction
ENSG00000186635	Chromatin interaction
ENSG00000186642	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10793036	0.81[CHB][hapmap]
rs10898866	0.92[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap]
rs11235557	0.86[ASN][1000 genomes]
rs11235558	0.86[ASN][1000 genomes]
rs11235559	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs11235569	0.85[CEU][hapmap]
rs11235575	0.92[CEU][hapmap]
rs11607038	0.84[JPT][hapmap]
rs12146545	1.00[CHB][hapmap]
rs12362256	0.84[ASN][1000 genomes]
rs12363065	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs12576046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12786302	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12787293	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797368	0.86[ASN][1000 genomes]
rs12797791	0.93[CHB][hapmap]
rs12799451	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12802369	0.98[ASN][1000 genomes]
rs12804316	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1391888	1.00[CHB][hapmap]
rs163694	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs168175	0.83[ASN][1000 genomes]
rs1872126	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs189332	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1980089	0.81[CHB][hapmap]
rs2035467	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2037030	0.86[ASN][1000 genomes]
rs2291289	0.85[CEU][hapmap]
rs2306607	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs2306609	0.87[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2306616	0.84[JPT][hapmap]
rs341052	0.93[CHB][hapmap]
rs341053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs341060	0.88[ASN][1000 genomes]
rs341061	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs341062	0.87[ASN][1000 genomes]
rs34142547	1.00[ASN][1000 genomes]
rs342322	0.86[ASN][1000 genomes]
rs34285624	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34802028	1.00[ASN][1000 genomes]
rs35748558	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758934	0.91[ASN][1000 genomes]
rs3758935	0.93[ASN][1000 genomes]
rs3758936	0.93[ASN][1000 genomes]
rs3781913	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs3781916	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs458275	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs458575	0.81[CHB][hapmap]
rs7110801	0.81[MEX][hapmap]
rs7125221	0.88[CEU][hapmap]
rs7126790	0.92[ASN][1000 genomes]
rs900613	0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs900614	0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs900615	0.91[ASN][1000 genomes]
rs90409	0.86[CHB][hapmap]

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	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
2	nsv832207	chr11:72272750-72469122	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
3	nsv523601	chr11:72281884-72430935	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
4	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12576058	ARAP1	cis	cerebellum	SCAN
rs12576058	KRTAP5-10	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72380600-72395400	Weak transcription	Right Atrium	heart
2	chr11:72388000-72397200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:72388200-72396400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr11:72388600-72395000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:72388600-72396000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:72389600-72397800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr11:72390000-72395200	Weak transcription	Liver	Liver
8	chr11:72390000-72397000	Weak transcription	Primary B cells from cord blood	blood
9	chr11:72390200-72397800	Weak transcription	HepG2	liver
10	chr11:72390400-72395200	Weak transcription	A549	lung
11	chr11:72390600-72395400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr11:72390800-72395000	Weak transcription	Fetal Brain Female	brain
13	chr11:72390800-72395000	Weak transcription	HSMMtube	muscle
14	chr11:72391200-72395000	Weak transcription	Adipose Nuclei	Adipose
15	chr11:72391200-72395000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:72391200-72395200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr11:72391200-72395200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:72391200-72396400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:72391400-72395800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr11:72391400-72403800	Weak transcription	Small Intestine	intestine
21	chr11:72391600-72394800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr11:72391800-72398600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:72392000-72395000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:72392000-72395200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:72392200-72402600	Weak transcription	HUVEC	blood vessel
26	chr11:72392400-72395400	Weak transcription	Brain Germinal Matrix	brain
27	chr11:72392600-72395000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr11:72392600-72395000	Weak transcription	NHDF-Ad	bronchial
29	chr11:72392600-72395200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:72392600-72395200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:72392600-72395400	Weak transcription	Stomach Mucosa	stomach
32	chr11:72392600-72395600	Weak transcription	Ovary	ovary
33	chr11:72392800-72394800	Weak transcription	Left Ventricle	heart
34	chr11:72392800-72395000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:72392800-72395000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:72392800-72395000	Weak transcription	Fetal Lung	lung
37	chr11:72392800-72395200	Weak transcription	NH-A	brain
38	chr11:72392800-72395400	Weak transcription	Right Ventricle	heart
39	chr11:72392800-72395600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:72392800-72395800	Weak transcription	Fetal Heart	heart
41	chr11:72392800-72396200	Weak transcription	Pancreas	Pancrea
42	chr11:72392800-72396800	Weak transcription	Fetal Brain Male	brain
43	chr11:72392800-72397200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr11:72392800-72397400	Weak transcription	Brain Anterior Caudate	brain
45	chr11:72392800-72404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr11:72392800-72404800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:72392800-72405600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr11:72393000-72394800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:72393000-72395000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr11:72393000-72395000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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