Variant report

Variant	rs1636250
Chromosome Location	chr7:2884433-2884434
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	MAX	chr7:2883501-2884512	K562	blood:	n/a	chr7:2883882-2883891
2	ATF1	chr7:2883937-2884453	K562	blood:	n/a	n/a
3	SP2	chr7:2883889-2884516	HepG2	liver:	n/a	chr7:2884188-2884203 chr7:2884114-2884129 chr7:2884051-2884061
4	ELK1	chr7:2883950-2884493	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:2884187-2884630	HepG2	liver:	n/a	n/a
6	EP300	chr7:2884171-2884826	K562	blood:	n/a	n/a
7	WRNIP1	chr7:2884252-2884641	GM12878	blood:	n/a	n/a
8	POLR2A	chr7:2883500-2884583	GM18505	blood:	n/a	n/a
9	SP2	chr7:2883919-2884453	H1-hESC	embryonic stem cell:	n/a	chr7:2884188-2884203 chr7:2884114-2884129 chr7:2884051-2884061
10	USF2	chr7:2884268-2884450	HepG2	liver:	n/a	n/a
11	YY1	chr7:2883805-2884489	SK-N-SH_RA	brain:	n/a	chr7:2883916-2883925 chr7:2883916-2883927 chr7:2883908-2883922
12	SP2	chr7:2883947-2884470	H1-hESC	embryonic stem cell:	n/a	chr7:2884188-2884203 chr7:2884114-2884129 chr7:2884051-2884061
13	RFX5	chr7:2883976-2884652	GM12878	blood:	n/a	n/a
14	UBTF	chr7:2884416-2884464	K562	blood:	n/a	n/a
15	FOS	chr7:2883872-2884437	GM12878	blood:	n/a	chr7:2884192-2884201 chr7:2884073-2884082
16	POLR2A	chr7:2884292-2884446	A549	lung:	n/a	n/a
17	POLR2A	chr7:2884169-2884531	HCT-116	colon:	n/a	n/a
18	EP300	chr7:2884345-2884729	K562	blood:	n/a	n/a
19	RUNX3	chr7:2884240-2884543	GM12878	blood:	n/a	n/a
20	POLR2A	chr7:2883903-2884862	PANC-1	pancreas:	n/a	n/a
21	FOXA2	chr7:2884134-2884527	A549	lung:	n/a	n/a
22	GTF2F1	chr7:2884286-2884649	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr7:2883918-2884574	GM12878	blood:	n/a	n/a
24	HCFC1	chr7:2883693-2884614	Hela-S3	cervix:	n/a	n/a
25	MAFK	chr7:2884233-2884759	K562	blood:	n/a	chr7:2884563-2884579 chr7:2884561-2884572 chr7:2884407-2884418 chr7:2884560-2884575 chr7:2884561-2884581
26	GATA3	chr7:2884162-2884605	T-47D	breast:	n/a	chr7:2884409-2884425 chr7:2884407-2884428 chr7:2884411-2884423 chr7:2884565-2884572 chr7:2884412-2884421 chr7:2884403-2884420
27	POLR2A	chr7:2884206-2884533	H1-hESC	embryonic stem cell:	n/a	n/a
28	ELF1	chr7:2883835-2884473	MCF-7	breast:	n/a	chr7:2883916-2883925 chr7:2883915-2883927 chr7:2883918-2883930
29	SP1	chr7:2883832-2884578	H1-hESC	embryonic stem cell:	n/a	chr7:2884192-2884204 chr7:2884193-2884202 chr7:2884206-2884220 chr7:2884488-2884502 chr7:2884098-2884107 chr7:2884097-2884109 chr7:2884192-2884204 chr7:2884193-2884203 chr7:2884209-2884220 chr7:2884209-2884221 chr7:2884099-2884108 chr7:2884098-2884108 chr7:2884099-2884108 chr7:2884097-2884109 chr7:2884194-2884203 chr7:2883884-2883894 chr7:2884192-2884203
30	MXI1	chr7:2884306-2884626	K562	blood:	n/a	n/a
31	SP1	chr7:2883890-2884689	A549	lung:	n/a	chr7:2884192-2884204 chr7:2884193-2884202 chr7:2884206-2884220 chr7:2884488-2884502 chr7:2884098-2884107 chr7:2884097-2884109 chr7:2884192-2884204 chr7:2884193-2884203 chr7:2884209-2884220 chr7:2884209-2884221 chr7:2884099-2884108 chr7:2884098-2884108 chr7:2884099-2884108 chr7:2884097-2884109 chr7:2884194-2884203 chr7:2884192-2884203
32	CREB1	chr7:2883559-2884479	A549	lung:	n/a	n/a
33	POLR2A	chr7:2883759-2884691	GM12878	blood:	n/a	n/a
34	BHLHE40	chr7:2883930-2884522	HepG2	liver:	n/a	n/a
35	POLR2A	chr7:2883429-2884614	MCF-7	breast:	n/a	n/a
36	ZNF143	chr7:2884038-2884808	K562	blood:	n/a	n/a
37	IRF1	chr7:2883870-2884701	K562	blood:	n/a	chr7:2884192-2884206
38	EBF1	chr7:2884027-2884511	GM12878	blood:	n/a	n/a
39	NFYA	chr7:2883831-2884507	K562	blood:	n/a	chr7:2884147-2884161 chr7:2884053-2884065 chr7:2884049-2884064 chr7:2884049-2884064 chr7:2884045-2884063 chr7:2884050-2884064
40	POLR2A	chr7:2883556-2884563	MCF10A-Er-Src	breast:	n/a	n/a
41	CREB1	chr7:2883847-2884490	H1-hESC	embryonic stem cell:	n/a	n/a
42	RFX5	chr7:2882892-2885962	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr7:2884187-2884498	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr7:2884226-2884517	H1-hESC	embryonic stem cell:	n/a	n/a
45	GTF2F1	chr7:2884334-2884445	K562	blood:	n/a	n/a
46	CEBPZ	chr7:2883967-2884577	HepG2	liver:	n/a	n/a
47	POLR2A	chr7:2883127-2884546	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr7:2883595-2884554	HepG2	liver:	n/a	n/a
49	MAZ	chr7:2883431-2884657	K562	blood:	n/a	chr7:2883882-2883891 chr7:2883465-2883475
50	POLR2A	chr7:2883622-2884578	NB4	blood:	n/a	n/a

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
ENSG00000178096	Chromatin interaction
ENSG00000231357	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000174945	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000184260	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1182143	0.82[CEU][hapmap]
rs1182155	0.95[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs1182174	0.84[CEU][hapmap]
rs1182179	0.81[GIH][hapmap]
rs1182181	0.81[GIH][hapmap]
rs1182183	0.81[CEU][hapmap]
rs1182188	0.81[GIH][hapmap]
rs1182198	0.81[CEU][hapmap]
rs1182199	0.81[EUR][1000 genomes]
rs11973498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12700373	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13230946	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13230995	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1614791	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636247	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1636248	0.92[ASN][1000 genomes]
rs1636249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636251	0.95[ASN][1000 genomes]
rs1636252	0.97[ASN][1000 genomes]
rs1636253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1636254	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1636255	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636256	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1636264	0.82[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1639034	0.96[ASN][1000 genomes]
rs1639036	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1639040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1639066	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1713912	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1713921	0.93[ASN][1000 genomes]
rs2107964	0.86[CEU][hapmap]
rs2527677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527680	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527681	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2533867	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533868	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533871	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533875	0.94[ASN][1000 genomes]
rs2533877	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533878	0.84[ASW][hapmap];0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs2533889	0.81[EUR][1000 genomes]
rs2533891	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644286	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644293	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644300	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644309	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2679259	0.96[ASN][1000 genomes]
rs71522301	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71522302	0.87[AMR][1000 genomes]
rs71524003	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7783400	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798485	0.81[TSI][hapmap]
rs798486	0.81[TSI][hapmap]
rs798490	0.81[TSI][hapmap]
rs798502	0.84[ASW][hapmap];0.81[TSI][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1636250	GNA12	cis	Artery Tibial	GTEx
rs1636250	MICALL2	cis	cerebellum	SCAN
rs1636250	GNA12	cis	Nerve Tibial	GTEx
rs1636250	GNA12	cis	lymphoblastoid	seeQTL
rs1636250	GNA12	cis	multi-tissue	Pritchard
rs1636250	GNA12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2882000-2884600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr7:2882400-2884800	Active TSS	NHLF	lung
3	chr7:2882400-2885000	Active TSS	A549	lung
4	chr7:2882600-2884600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr7:2882600-2884600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:2882600-2884800	Active TSS	HSMM	muscle
7	chr7:2882800-2884800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr7:2883000-2884600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr7:2883000-2884600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:2883000-2884600	Active TSS	NHDF-Ad	bronchial
11	chr7:2883000-2884800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:2883000-2884800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:2883200-2884600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr7:2883200-2884600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:2883200-2884600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:2883200-2884600	Active TSS	Aorta	Aorta
17	chr7:2883200-2884600	Active TSS	Esophagus	oesophagus
18	chr7:2883200-2884600	Active TSS	Ovary	ovary
19	chr7:2883200-2884600	Active TSS	Placenta Amnion	Placenta Amnion
20	chr7:2883200-2884600	Active TSS	Right Atrium	heart
21	chr7:2883200-2884600	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr7:2883200-2884800	Active TSS	Brain Angular Gyrus	brain
23	chr7:2883200-2884800	Active TSS	Brain Cingulate Gyrus	brain
24	chr7:2883200-2884800	Active TSS	Brain Hippocampus Middle	brain
25	chr7:2883200-2884800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr7:2883200-2884800	Active TSS	Colon Smooth Muscle	Colon
27	chr7:2883200-2884800	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr7:2883200-2884800	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr7:2883200-2884800	Active TSS	Rectal Smooth Muscle	rectum
30	chr7:2883200-2884800	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr7:2883400-2884600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr7:2883400-2884600	Active TSS	Left Ventricle	heart
33	chr7:2883400-2884800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr7:2883400-2884800	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr7:2883400-2884800	Active TSS	Thymus	Thymus
36	chr7:2884200-2884600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr7:2884200-2884600	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr7:2884200-2884600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr7:2884200-2884600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr7:2884200-2884600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:2884200-2884600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:2884200-2884600	Flanking Active TSS	Liver	Liver
43	chr7:2884200-2884600	Active TSS	Fetal Brain Male	brain
44	chr7:2884200-2884600	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr7:2884200-2884600	Flanking Active TSS	Lung	lung
46	chr7:2884200-2884600	Flanking Active TSS	HUVEC	blood vessel
47	chr7:2884200-2884600	Flanking Active TSS	Osteobl	bone
48	chr7:2884200-2884800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr7:2884200-2884800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr7:2884200-2884800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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