Variant report

Variant	rs1636251
Chromosome Location	chr7:2884720-2884721
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	EP300	chr7:2884171-2884826	K562	blood:	n/a	n/a
2	CEBPB	chr7:2884523-2884849	A549	lung:	n/a	chr7:2884693-2884704
3	EP300	chr7:2884345-2884729	K562	blood:	n/a	n/a
4	POLR2A	chr7:2883903-2884862	PANC-1	pancreas:	n/a	n/a
5	MAFK	chr7:2884233-2884759	K562	blood:	n/a	chr7:2884563-2884579 chr7:2884561-2884572 chr7:2884407-2884418 chr7:2884560-2884575 chr7:2884561-2884581
6	ZNF143	chr7:2884038-2884808	K562	blood:	n/a	n/a
7	CEBPB	chr7:2884642-2884817	HepG2	liver:	n/a	chr7:2884693-2884704
8	RFX5	chr7:2882892-2885962	SK-N-SH	brain:	n/a	n/a
9	BHLHE40	chr7:2883910-2885058	K562	blood:	n/a	chr7:2883924-2883940 chr7:2883916-2883932
10	MAFK	chr7:2884152-2884776	HepG2	liver:	n/a	chr7:2884563-2884579 chr7:2884561-2884572 chr7:2884407-2884418 chr7:2884560-2884575 chr7:2884561-2884581
11	POLR2A	chr7:2882980-2884959	HepG2	liver:	n/a	n/a
12	BACH1	chr7:2884096-2884747	H1-hESC	embryonic stem cell:	n/a	n/a
13	CEBPB	chr7:2883973-2884874	K562	blood:	n/a	chr7:2884053-2884061 chr7:2884693-2884704
14	MAX	chr7:2883284-2884733	A549	lung:	n/a	chr7:2883882-2883891 chr7:2883465-2883475
15	RFX5	chr7:2884189-2884739	H1-hESC	embryonic stem cell:	n/a	n/a
16	GATA2	chr7:2884130-2885050	SH-SY5Y	brain:	n/a	chr7:2884409-2884425 chr7:2884407-2884428 chr7:2884411-2884423 chr7:2884565-2884572 chr7:2884412-2884421 chr7:2884403-2884420
17	CEBPB	chr7:2884405-2884851	H1-hESC	embryonic stem cell:	n/a	chr7:2884693-2884704
18	SMC3	chr7:2884717-2884947	HepG2	liver:	n/a	n/a
19	MXI1	chr7:2883299-2885027	IMR90	lung:	n/a	n/a
20	RFX5	chr7:2884140-2884765	K562	blood:	n/a	n/a
21	CHD1	chr7:2882681-2884736	IMR90	lung:	n/a	n/a
22	POLR2A	chr7:2884187-2884747	GM12891	blood:	n/a	n/a
23	POLR2A	chr7:2883695-2884730	H1-hESC	embryonic stem cell:	n/a	n/a
24	NFYB	chr7:2883822-2884750	GM12878	blood:	n/a	chr7:2884147-2884161 chr7:2884053-2884065 chr7:2884049-2884064 chr7:2884049-2884064 chr7:2884050-2884064
25	MAFK	chr7:2884175-2884760	HepG2	liver:	n/a	chr7:2884563-2884579 chr7:2884561-2884572 chr7:2884407-2884418 chr7:2884560-2884575 chr7:2884561-2884581
26	REST	chr7:2883163-2884841	H1-neurons	neurons:	n/a	chr7:2883461-2883474 chr7:2883882-2883895 chr7:2883464-2883477
27	MAZ	chr7:2883802-2884777	GM12878	blood:	n/a	chr7:2883882-2883891
28	MXI1	chr7:2883467-2884797	GM12878	blood:	n/a	n/a
29	TCF7L2	chr7:2884664-2885248	MCF-7	breast:	n/a	n/a
30	RCOR1	chr7:2883918-2884969	K562	blood:	n/a	n/a
31	CEBPB	chr7:2884445-2884819	A549	lung:	n/a	chr7:2884693-2884704
32	POLR2A	chr7:2883865-2884937	HepG2	liver:	n/a	n/a
33	MAFF	chr7:2884206-2884740	HepG2	liver:	n/a	chr7:2884558-2884576
34	NR2F2	chr7:2883982-2884721	K562	blood:	n/a	n/a
35	MAFK	chr7:2884252-2884873	H1-hESC	embryonic stem cell:	n/a	chr7:2884563-2884579 chr7:2884561-2884572 chr7:2884407-2884418 chr7:2884560-2884575 chr7:2884561-2884581
36	CEBPB	chr7:2883966-2884907	MCF-7	breast:	n/a	chr7:2884053-2884061 chr7:2884693-2884704
37	BACH1	chr7:2884324-2884729	K562	blood:	n/a	n/a
38	MTA3	chr7:2884221-2884730	GM12878	blood:	n/a	n/a
39	MAFK	chr7:2884151-2884740	IMR90	lung:	n/a	chr7:2884563-2884579 chr7:2884561-2884572 chr7:2884407-2884418 chr7:2884560-2884575 chr7:2884561-2884581

No.	Distal block	Cell Line	Cell type
1	chr7:2884125..2886886-chr7:2909522..2911680,2	MCF-7	breast:
2	chr1:149858014..149859677-chr7:2882924..2885730,2	MCF-7	breast:
3	chr7:2869377..2877481-chr7:2880306..2885399,15	MCF-7	breast:
4	chr7:2878232..2880029-chr7:2884178..2886023,2	MCF-7	breast:
5	chr7:2726313..2732670-chr7:2878755..2886203,10	MCF-7	breast:

Variant related genes	Relation type
GNA12	TF binding region
ENSG00000184678	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000231357	Chromatin interaction
ENSG00000174945	Chromatin interaction
ENSG00000184270	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1182156	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11973498	0.94[ASN][1000 genomes]
rs12700373	0.93[ASN][1000 genomes]
rs13230995	0.94[ASN][1000 genomes]
rs1614791	0.92[ASN][1000 genomes]
rs1623138	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1636247	0.90[ASN][1000 genomes]
rs1636248	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1636249	0.95[ASN][1000 genomes]
rs1636250	0.95[ASN][1000 genomes]
rs1636252	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636253	0.94[ASN][1000 genomes]
rs1636254	0.94[ASN][1000 genomes]
rs1636255	0.92[ASN][1000 genomes]
rs1636256	0.84[ASN][1000 genomes]
rs1639034	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1639036	0.95[ASN][1000 genomes]
rs1639040	0.95[ASN][1000 genomes]
rs1639064	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1639065	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1639066	0.92[ASN][1000 genomes]
rs1713913	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1713921	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2527677	0.93[ASN][1000 genomes]
rs2527680	0.92[ASN][1000 genomes]
rs2527681	0.91[ASN][1000 genomes]
rs2533867	0.94[ASN][1000 genomes]
rs2533868	0.94[ASN][1000 genomes]
rs2533870	0.94[ASN][1000 genomes]
rs2533871	0.93[ASN][1000 genomes]
rs2533875	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533877	0.92[ASN][1000 genomes]
rs2533891	0.92[ASN][1000 genomes]
rs2644281	0.94[ASN][1000 genomes]
rs2644286	0.94[ASN][1000 genomes]
rs2644293	0.92[ASN][1000 genomes]
rs2644300	0.93[ASN][1000 genomes]
rs2644309	0.92[ASN][1000 genomes]
rs2679259	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71522301	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1018162	chr7:2817460-2891181	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv538655	chr7:2817460-2891181	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv887313	chr7:2875420-2927120	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv887314	chr7:2875420-2944187	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv3333602	chr7:2882776-2885274	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1636251	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs1636251	GNA12	cis	Nerve Tibial	GTEx
rs1636251	GNA12	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2882400-2884800	Active TSS	NHLF	lung
2	chr7:2882400-2885000	Active TSS	A549	lung
3	chr7:2882600-2884800	Active TSS	HSMM	muscle
4	chr7:2882800-2884800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr7:2883000-2884800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:2883000-2884800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:2883200-2884800	Active TSS	Brain Angular Gyrus	brain
8	chr7:2883200-2884800	Active TSS	Brain Cingulate Gyrus	brain
9	chr7:2883200-2884800	Active TSS	Brain Hippocampus Middle	brain
10	chr7:2883200-2884800	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr7:2883200-2884800	Active TSS	Colon Smooth Muscle	Colon
12	chr7:2883200-2884800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr7:2883200-2884800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr7:2883200-2884800	Active TSS	Rectal Smooth Muscle	rectum
15	chr7:2883200-2884800	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr7:2883400-2884800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:2883400-2884800	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr7:2883400-2884800	Active TSS	Thymus	Thymus
19	chr7:2884200-2884800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr7:2884200-2884800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr7:2884200-2884800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr7:2884200-2884800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr7:2884200-2884800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:2884200-2884800	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr7:2884200-2884800	Enhancers	Small Intestine	intestine
26	chr7:2884200-2884800	Flanking Active TSS	Dnd41	blood
27	chr7:2884200-2884800	Flanking Active TSS	Hela-S3	cervix
28	chr7:2884200-2884800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr7:2884200-2885000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr7:2884200-2885000	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr7:2884400-2884800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr7:2884400-2884800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:2884400-2884800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:2884400-2884800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr7:2884400-2884800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr7:2884400-2884800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr7:2884400-2884800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr7:2884400-2884800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:2884400-2884800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr7:2884400-2884800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr7:2884400-2884800	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr7:2884400-2884800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr7:2884400-2884800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr7:2884400-2884800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr7:2884400-2884800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:2884400-2884800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:2884400-2884800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:2884400-2884800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:2884400-2884800	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr7:2884400-2884800	Flanking Active TSS	Brain Substantia Nigra	brain

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