Variant report

Variant	rs12534109
Chromosome Location	chr7:65613650-65613651
allele	C/T
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	MTA3	chr7:65613227-65613934	GM12878	blood:	n/a	n/a
2	ZKSCAN1	chr7:65613503-65613802	Hela-S3	cervix:	n/a	n/a
3	TCF12	chr7:65613237-65614108	SK-N-SH	brain:	n/a	chr7:65613508-65613515
4	MYC	chr7:65613435-65613991	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr7:65613525-65614005	Hela-S3	cervix:	n/a	n/a
6	JUND	chr7:65613236-65614051	SK-N-SH	brain:	n/a	chr7:65613590-65613600 chr7:65613592-65613603 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613590-65613600
7	MAX	chr7:65613431-65613891	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr7:65613447-65613845	IMR90	lung:	n/a	n/a
9	POLR2A	chr7:65613404-65613920	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr7:65613479-65613795	GM12878	blood:	n/a	n/a
11	SP1	chr7:65613237-65614043	HCT-116	colon:	n/a	n/a
12	NR3C1	chr7:65613454-65613780	A549	lung:	n/a	chr7:65613587-65613594 chr7:65613591-65613600
13	POLR2A	chr7:65613487-65613782	K562	blood:	n/a	n/a
14	JUN	chr7:65613444-65613856	HUVEC	blood vessel:	n/a	chr7:65613590-65613600 chr7:65613592-65613603 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613590-65613600
15	JUND	chr7:65613510-65613710	K562	blood:	n/a	chr7:65613590-65613600 chr7:65613592-65613603 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613590-65613600
16	BHLHE40	chr7:65613633-65613745	K562	blood:	n/a	n/a
17	PBX3	chr7:65613312-65613975	SK-N-SH	brain:	n/a	n/a
18	EP300	chr7:65613385-65613827	SK-N-SH_RA	brain:	n/a	n/a
19	BRCA1	chr7:65613453-65613964	Hela-S3	cervix:	n/a	n/a
20	RCOR1	chr7:65613440-65613816	Hela-S3	cervix:	n/a	n/a
21	STAT3	chr7:65613439-65613928	MCF10A-Er-Src	breast:	n/a	n/a
22	GATA3	chr7:65613267-65614050	SK-N-SH	brain:	n/a	chr7:65613946-65613953
23	RUNX3	chr7:65613417-65613940	GM12878	blood:	n/a	n/a
24	CEBPB	chr7:65613404-65613946	Hela-S3	cervix:	n/a	n/a
25	MYC	chr7:65613601-65613804	Hela-S3	cervix:	n/a	n/a
26	GATA3	chr7:65613277-65614126	SK-N-SH	brain:	n/a	chr7:65613946-65613953
27	CREB1	chr7:65613210-65614040	GM12878	blood:	n/a	n/a
28	NR2F2	chr7:65613499-65613834	K562	blood:	n/a	n/a
29	JUND	chr7:65613368-65614029	SK-N-SH	brain:	n/a	chr7:65613590-65613600 chr7:65613592-65613603 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613590-65613600
30	FOSL1	chr7:65613189-65614103	HCT-116	colon:	n/a	chr7:65613590-65613600 chr7:65613592-65613603 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613590-65613600
31	PBX3	chr7:65613368-65613980	SK-N-SH	brain:	n/a	n/a
32	GATA2	chr7:65613380-65613865	HUVEC	blood vessel:	n/a	n/a
33	RFX5	chr7:65613417-65613816	Hela-S3	cervix:	n/a	n/a
34	NR3C1	chr7:65613415-65613888	A549	lung:	n/a	chr7:65613587-65613594 chr7:65613591-65613600
35	JUN	chr7:65613407-65613927	Hela-S3	cervix:	n/a	chr7:65613590-65613600 chr7:65613592-65613603 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613590-65613600
36	JUND	chr7:65613483-65613748	HepG2	liver:	n/a	chr7:65613590-65613600 chr7:65613592-65613603 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613590-65613600
37	FOS	chr7:65613378-65613867	HUVEC	blood vessel:	n/a	chr7:65613590-65613600 chr7:65613592-65613603 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613589-65613600
38	POLR2A	chr7:65613444-65613838	HCT-116	colon:	n/a	n/a
39	TCF12	chr7:65613220-65614030	SK-N-SH	brain:	n/a	chr7:65613508-65613515
40	EP300	chr7:65613393-65613892	SK-N-SH_RA	brain:	n/a	n/a
41	FOSL2	chr7:65613266-65614042	SK-N-SH	brain:	n/a	chr7:65613590-65613600 chr7:65613592-65613603 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613590-65613600
42	FOS	chr7:65613398-65613976	MCF10A-Er-Src	breast:	n/a	chr7:65613590-65613600 chr7:65613592-65613603 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613590-65613600 chr7:65613589-65613600
43	ELK1	chr7:65613515-65613799	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr7:65613436-65613857	Hela-S3	cervix:	n/a	n/a
45	ARID3A	chr7:65613601-65613844	HepG2	liver:	n/a	n/a
46	YY1	chr7:65613396-65613742	HCT-116	colon:	n/a	n/a
47	E2F4	chr7:65613468-65613853	MCF10A-Er-Src	breast:	n/a	n/a
48	NFATC1	chr7:65613353-65613981	GM12878	blood:	n/a	n/a
49	FOXP2	chr7:65613463-65613764	PFSK-1	brain:	n/a	n/a
50	RAD21	chr7:65613368-65613891	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65613342..65615029-chr7:65615766..65618205,2	MCF-7	breast:
2	chr7:65610382..65612818-chr7:65612970..65615484,3	K562	blood:

Variant related genes	Relation type
CRCP	TF binding region

Extended variants
information (count: 103 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs12530506	0.87[EUR][1000 genomes]
rs12530898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs12531358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12531900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12532327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs12532423	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12532675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12534477	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12534881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12535985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536292	0.84[ASN][1000 genomes]
rs12536816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12537039	0.89[EUR][1000 genomes]
rs12537407	0.84[ASN][1000 genomes]
rs12537698	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12537936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538025	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12538147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12538961	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12540307	0.80[EUR][1000 genomes]
rs12540888	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1363056	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2279904	1.00[AFR][1000 genomes]
rs2292936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35832738	1.00[AFR][1000 genomes]
rs35910256	0.89[EUR][1000 genomes]
rs3735141	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs3735145	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3815684	0.89[EUR][1000 genomes]
rs4149467	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465362	0.89[EUR][1000 genomes]
rs62465363	0.84[EUR][1000 genomes]
rs62465364	0.87[EUR][1000 genomes]
rs62465365	0.85[EUR][1000 genomes]
rs62465367	0.87[EUR][1000 genomes]
rs62465474	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465475	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465476	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465512	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465513	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465515	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465525	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465526	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465527	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465542	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465545	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62465546	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465547	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465550	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465552	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465554	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467382	1.00[AFR][1000 genomes]
rs62467384	1.00[AFR][1000 genomes]
rs62467385	1.00[AFR][1000 genomes]
rs62467386	1.00[AFR][1000 genomes]
rs62467410	1.00[AFR][1000 genomes]
rs62467411	1.00[AFR][1000 genomes]
rs62467413	1.00[AFR][1000 genomes]
rs62467414	1.00[AFR][1000 genomes]
rs62467421	1.00[AFR][1000 genomes]
rs62467437	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62467441	0.84[ASN][1000 genomes]
rs62467442	0.84[ASN][1000 genomes]
rs62467444	0.84[ASN][1000 genomes]
rs62467450	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs62468669	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62468673	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62468674	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62468677	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62468679	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62468696	0.89[EUR][1000 genomes]
rs62468699	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62468700	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62468702	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62468705	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62468707	0.87[EUR][1000 genomes]
rs62468708	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62468709	0.81[EUR][1000 genomes]
rs62468711	0.89[EUR][1000 genomes]
rs62468712	0.84[EUR][1000 genomes]
rs62470897	1.00[AFR][1000 genomes]
rs62470899	1.00[AFR][1000 genomes]
rs62470900	1.00[AFR][1000 genomes]
rs62470921	1.00[AFR][1000 genomes]
rs62470922	1.00[AFR][1000 genomes]
rs62470924	1.00[AFR][1000 genomes]
rs62470925	1.00[AFR][1000 genomes]
rs62470926	1.00[AFR][1000 genomes]
rs62470931	1.00[AFR][1000 genomes]
rs62470934	1.00[AFR][1000 genomes]
rs62470940	1.00[AFR][1000 genomes]
rs62470945	1.00[AFR][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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv971489	chr7:65590579-65614004	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12534109	hmm32897	cis	multi-tissue	Pritchard
rs12534109	RABGEF1	cis	multi-tissue	Pritchard
rs12534109	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs12534109	RABGEF1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65581000-65617200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:65594800-65614400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr7:65595000-65614400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr7:65595000-65614600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr7:65595000-65615200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:65595200-65614000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:65595200-65622000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:65595600-65623200	Strong transcription	Dnd41	blood
9	chr7:65595600-65623800	Strong transcription	Primary T cells from cord blood	blood
10	chr7:65595800-65617200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:65595800-65620000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:65599200-65614200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:65599200-65623400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr7:65604200-65614000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:65604400-65613800	Strong transcription	Fetal Thymus	thymus
16	chr7:65604600-65613800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr7:65605800-65615200	Strong transcription	K562	blood
18	chr7:65606600-65613800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:65606600-65614400	Strong transcription	Fetal Brain Female	brain
20	chr7:65606600-65617600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:65606800-65614200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:65607400-65613800	Strong transcription	Brain Anterior Caudate	brain
23	chr7:65607400-65617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:65608000-65613800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:65608200-65617000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:65608400-65615400	Weak transcription	Stomach Mucosa	stomach
27	chr7:65608600-65615600	Weak transcription	HSMMtube	muscle
28	chr7:65608800-65614600	Strong transcription	Fetal Intestine Large	intestine
29	chr7:65609000-65622400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:65609200-65615400	Weak transcription	Fetal Heart	heart
31	chr7:65609200-65615800	Weak transcription	Psoas Muscle	Psoas
32	chr7:65609200-65623200	Weak transcription	Fetal Brain Male	brain
33	chr7:65609200-65623400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:65609400-65614000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:65609600-65624600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr7:65610000-65613800	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr7:65610200-65614200	Genic enhancers	HepG2	liver
38	chr7:65610200-65615800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:65610400-65617000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr7:65610800-65614000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr7:65611200-65614000	Strong transcription	Placenta	Placenta
42	chr7:65611200-65615400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:65611200-65615400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:65611200-65615600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr7:65611200-65615600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr7:65611200-65615800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:65611200-65617000	Enhancers	NHDF-Ad	bronchial
48	chr7:65611400-65615400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr7:65611400-65615600	Weak transcription	Ovary	ovary
50	chr7:65611800-65615400	Weak transcription	Primary B cells from cord blood	blood

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