Variant report

Variant	rs2533879
Chromosome Location	chr7:2859847-2859848
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	RCOR1	chr7:2859692-2862101	IMR90	lung:	n/a	n/a
2	FOXA2	chr7:2859822-2860033	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:2726641..2729918-chr7:2858663..2861748,4	MCF-7	breast:
2	chr7:2857088..2858665-chr7:2859530..2861799,2	K562	blood:
3	chr7:2855867..2858678-chr7:2858785..2861343,3	MCF-7	breast:
4	chr7:2796001..2798506-chr7:2858838..2860975,2	MCF-7	breast:
5	chr7:2852392..2854635-chr7:2859767..2862192,2	K562	blood:

Variant related genes	Relation type
GNA12	TF binding region
ENSG00000174945	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1182172	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1182174	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1182176	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1182177	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1182178	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1182179	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1182181	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1182182	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1182183	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1182184	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1182185	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1182186	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1182187	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1182188	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1182189	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1182196	0.88[ASN][1000 genomes]
rs1182198	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1182199	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182207	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1182208	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1182209	0.81[ASN][1000 genomes]
rs1183085	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13243214	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1636247	0.84[EUR][1000 genomes]
rs1636264	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1713919	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2107964	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2158694	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2248390	0.94[ASN][1000 genomes]
rs2251491	0.94[ASN][1000 genomes]
rs2260230	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2266922	0.86[ASN][1000 genomes]
rs2283779	0.84[ASN][1000 genomes]
rs2283783	0.94[ASN][1000 genomes]
rs2283784	0.94[ASN][1000 genomes]
rs2527683	0.87[ASN][1000 genomes]
rs2527684	0.87[ASN][1000 genomes]
rs2527687	0.94[ASN][1000 genomes]
rs2527690	0.98[ASN][1000 genomes]
rs2527692	0.94[ASN][1000 genomes]
rs2527694	0.95[ASN][1000 genomes]
rs2527695	0.95[ASN][1000 genomes]
rs2527696	0.95[ASN][1000 genomes]
rs2533878	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2533882	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2533884	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2644274	0.94[ASN][1000 genomes]
rs2644275	0.94[ASN][1000 genomes]
rs2644294	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2644295	0.96[ASN][1000 genomes]
rs2644296	0.95[ASN][1000 genomes]
rs2644297	0.95[ASN][1000 genomes]
rs2644298	0.95[ASN][1000 genomes]
rs2644309	0.82[EUR][1000 genomes]
rs2644312	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35957220	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6970963	0.85[ASN][1000 genomes]
rs6978692	0.94[ASN][1000 genomes]
rs757791	0.91[ASN][1000 genomes]
rs7777484	0.83[ASN][1000 genomes]
rs7790322	0.83[AFR][1000 genomes]
rs7807978	0.83[ASN][1000 genomes]
rs798480	0.81[ASN][1000 genomes]
rs798482	0.81[ASN][1000 genomes]
rs798485	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs798486	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs798487	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs798488	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798489	0.82[EUR][1000 genomes]
rs798490	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798491	0.87[EUR][1000 genomes]
rs798493	0.87[EUR][1000 genomes]
rs798494	0.87[EUR][1000 genomes]
rs798495	0.86[EUR][1000 genomes]
rs798497	0.87[EUR][1000 genomes]
rs798498	0.81[EUR][1000 genomes]
rs798500	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs798502	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs798508	0.81[EUR][1000 genomes]
rs798511	0.83[EUR][1000 genomes]
rs798514	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs798526	0.81[EUR][1000 genomes]
rs960273	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv1019463	chr7:2848448-2881872	Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2533879	GNA12	cis	multi-tissue	Pritchard
rs2533879	GNA12	cis	Artery Tibial	GTEx
rs2533879	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2533879	GNA12	cis	Nerve Tibial	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2842600-2869400	Weak transcription	Primary T cells from cord blood	blood
2	chr7:2843000-2860800	Weak transcription	Esophagus	oesophagus
3	chr7:2843200-2860800	Weak transcription	HSMMtube	muscle
4	chr7:2843200-2864400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr7:2843600-2860600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:2843600-2864400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr7:2845800-2862200	Weak transcription	K562	blood
8	chr7:2848600-2864000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:2848800-2863400	Weak transcription	Fetal Brain Female	brain
10	chr7:2848800-2874800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:2849400-2860800	Weak transcription	Stomach Mucosa	stomach
12	chr7:2849600-2866000	Enhancers	Placenta	Placenta
13	chr7:2851000-2860200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:2851600-2860600	Weak transcription	Primary B cells from cord blood	blood
15	chr7:2851600-2861000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr7:2851600-2861000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:2851600-2869600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:2851800-2860400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
20	chr7:2852000-2860400	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:2853200-2860600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:2854000-2874800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:2854600-2860600	Weak transcription	Fetal Kidney	kidney
24	chr7:2854600-2861000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr7:2854800-2860200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:2854800-2860200	Weak transcription	Colonic Mucosa	Colon
27	chr7:2855800-2860200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:2855800-2860800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr7:2855800-2860800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr7:2855800-2863600	Weak transcription	Brain Angular Gyrus	brain
31	chr7:2857000-2864600	Enhancers	H1 Cell Line	embryonic stem cell
32	chr7:2857000-2865000	Enhancers	Ovary	ovary
33	chr7:2857000-2867000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:2857200-2860400	Enhancers	A549	lung
35	chr7:2857200-2861600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr7:2857200-2861800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:2857200-2861800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr7:2857200-2862000	Enhancers	Adipose Nuclei	Adipose
39	chr7:2857200-2862000	Enhancers	Colon Smooth Muscle	Colon
40	chr7:2857200-2864200	Enhancers	NHDF-Ad	bronchial
41	chr7:2857200-2865400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:2858000-2860000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr7:2858000-2864000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr7:2858200-2860200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr7:2858200-2860600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:2858200-2860600	Weak transcription	Brain Germinal Matrix	brain
47	chr7:2858200-2861200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr7:2858200-2861600	Enhancers	Fetal Heart	heart
49	chr7:2858200-2862600	Enhancers	Right Atrium	heart
50	chr7:2858200-2863400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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