Variant report

Variant	rs2533884
Chromosome Location	chr7:2836848-2836849
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2835435..2836946-chr7:2841542..2843166,2	MCF-7	breast:
2	chr7:2834982..2836985-chr7:2838471..2841114,3	MCF-7	breast:
3	chr7:2836297..2839698-chr7:2841908..2844688,4	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1182172	0.86[EUR][1000 genomes]
rs1182174	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182176	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1182177	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182178	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1182179	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1182181	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182182	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182183	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182184	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1182185	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182186	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182187	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1182188	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1182189	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1182198	0.90[EUR][1000 genomes]
rs1182199	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182207	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1182208	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1183085	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13243214	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1636264	0.87[EUR][1000 genomes]
rs1713919	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2107964	0.90[EUR][1000 genomes]
rs2158694	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2260230	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2527687	0.85[ASN][1000 genomes]
rs2527690	0.81[ASN][1000 genomes]
rs2533878	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2533879	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2533882	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2644294	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2644312	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35957220	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798485	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798486	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798487	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798488	0.92[EUR][1000 genomes]
rs798489	0.86[EUR][1000 genomes]
rs798490	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs798491	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798493	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798494	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798495	0.90[EUR][1000 genomes]
rs798496	0.82[EUR][1000 genomes]
rs798497	0.92[EUR][1000 genomes]
rs798498	0.85[EUR][1000 genomes]
rs798500	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs798502	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs798506	0.82[EUR][1000 genomes]
rs798508	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs798511	0.87[EUR][1000 genomes]
rs798514	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs798518	0.81[EUR][1000 genomes]
rs798526	0.85[EUR][1000 genomes]
rs798528	0.83[EUR][1000 genomes]
rs960273	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2533884	GNA12	cis	Artery Tibial	GTEx
rs2533884	GNA12	cis	Nerve Tibial	GTEx
rs2533884	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2533884	GNA12	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2810600-2842600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:2810800-2840800	Weak transcription	Stomach Mucosa	stomach
3	chr7:2814400-2838800	Weak transcription	K562	blood
4	chr7:2815800-2840600	Weak transcription	Fetal Brain Male	brain
5	chr7:2822600-2841000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:2824000-2842800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:2829800-2841200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:2829800-2841400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:2830000-2841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:2830200-2842800	Weak transcription	Colonic Mucosa	Colon
11	chr7:2832000-2841400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr7:2832800-2841000	Weak transcription	NHEK	skin
13	chr7:2832800-2842600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:2833000-2840600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:2833000-2840800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:2833000-2842400	Weak transcription	Spleen	Spleen
17	chr7:2833200-2840800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr7:2833200-2842400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:2834000-2838400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:2834000-2840600	Weak transcription	Esophagus	oesophagus
21	chr7:2834000-2840800	Weak transcription	HMEC	breast
22	chr7:2834200-2840000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr7:2834200-2840800	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:2834200-2841000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:2834200-2841200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr7:2834400-2837000	Enhancers	Ovary	ovary
27	chr7:2834600-2837400	Enhancers	Right Atrium	heart
28	chr7:2834600-2838800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:2834600-2840200	Weak transcription	Fetal Brain Female	brain
30	chr7:2834600-2840200	Weak transcription	Fetal Thymus	thymus
31	chr7:2834600-2840800	Weak transcription	Hela-S3	cervix
32	chr7:2834600-2840800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr7:2834600-2841000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr7:2834600-2841400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:2834600-2842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:2834600-2847800	Weak transcription	Liver	Liver
37	chr7:2834800-2837200	Weak transcription	A549	lung
38	chr7:2834800-2839000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr7:2834800-2839000	Weak transcription	GM12878-XiMat	blood
40	chr7:2834800-2839400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr7:2834800-2840200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:2834800-2840400	Weak transcription	Fetal Intestine Small	intestine
43	chr7:2834800-2840800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr7:2834800-2840800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:2834800-2841000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr7:2834800-2841000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr7:2834800-2841000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr7:2834800-2841400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr7:2834800-2842200	Weak transcription	Brain Germinal Matrix	brain
50	chr7:2834800-2842400	Weak transcription	Rectal Mucosa Donor 31	rectum

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