Variant report

Variant	rs757786
Chromosome Location	chr7:2836019-2836020
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	CEBPB	chr7:2836005-2836713	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2835435..2836946-chr7:2841542..2843166,2	MCF-7	breast:
2	chr7:2834982..2836985-chr7:2838471..2841114,3	MCF-7	breast:

Variant related genes	Relation type
GNA12	TF binding region

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

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

rs_ID	r²[population]
rs1182175	1.00[YRI][hapmap]
rs1182180	0.84[AFR][1000 genomes]
rs1182190	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs1182191	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs1182192	0.86[AFR][1000 genomes]
rs1182193	0.86[AFR][1000 genomes]
rs1182194	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs1182206	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1182209	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1636264	0.96[YRI][hapmap]
rs208346	0.84[JPT][hapmap]
rs208356	0.83[CHB][hapmap]
rs2248390	0.87[AFR][1000 genomes]
rs2251491	0.84[AFR][1000 genomes]
rs2255541	0.82[CHB][hapmap]
rs2255782	0.82[CHB][hapmap]
rs2258709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2258960	0.91[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs2266922	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2266923	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2283784	0.85[AFR][1000 genomes]
rs2527686	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527689	0.86[CHB][hapmap]
rs2527690	0.96[YRI][hapmap]
rs2527695	0.88[AFR][1000 genomes]
rs2527696	0.87[AFR][1000 genomes]
rs2533885	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533890	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2644272	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2644274	0.96[YRI][hapmap]
rs2644275	0.88[YRI][hapmap]
rs2644295	0.88[YRI][hapmap]
rs2644296	0.92[YRI][hapmap]
rs2644297	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2644306	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2644307	0.94[ASN][1000 genomes]
rs2644311	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs3846992	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs6970963	0.85[AFR][1000 genomes]
rs6978692	0.88[AFR][1000 genomes]
rs709280	0.86[CHB][hapmap]
rs757787	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757791	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs7790322	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7807978	0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs798499	0.84[YRI][hapmap]
rs798503	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs798515	0.81[CHB][hapmap]
rs798517	0.82[CHB][hapmap]
rs798519	0.83[CHB][hapmap]
rs798521	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs798522	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs798525	0.83[CHB][hapmap]
rs798527	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs798530	0.82[CHB][hapmap]

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
rs757786	GNA12	cis	Artery Tibial	GTEx
rs757786		cis	Lymphoblastoid	GTEx
rs757786	LOC392620	cis	multi-tissue	Pritchard
rs757786	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr7:2824400-2836600	Weak transcription	Small Intestine	intestine
8	chr7:2828000-2836600	Weak transcription	Psoas Muscle	Psoas
9	chr7:2829800-2841200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:2829800-2841400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:2830000-2841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:2830200-2842800	Weak transcription	Colonic Mucosa	Colon
13	chr7:2830400-2836200	Weak transcription	Fetal Heart	heart
14	chr7:2832000-2841400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr7:2832800-2841000	Weak transcription	NHEK	skin
16	chr7:2832800-2842600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr7:2833000-2836600	Weak transcription	Lung	lung
18	chr7:2833000-2836600	Weak transcription	Pancreas	Pancrea
19	chr7:2833000-2836800	Weak transcription	Gastric	stomach
20	chr7:2833000-2840600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:2833000-2840800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr7:2833000-2842400	Weak transcription	Spleen	Spleen
23	chr7:2833200-2836200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:2833200-2840800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr7:2833200-2842400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:2834000-2836400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:2834000-2838400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:2834000-2840600	Weak transcription	Esophagus	oesophagus
29	chr7:2834000-2840800	Weak transcription	HMEC	breast
30	chr7:2834200-2836200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr7:2834200-2840000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:2834200-2840800	Weak transcription	Colon Smooth Muscle	Colon
33	chr7:2834200-2841000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:2834200-2841200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:2834400-2836400	Weak transcription	Brain Hippocampus Middle	brain
36	chr7:2834400-2837000	Enhancers	Ovary	ovary
37	chr7:2834600-2836400	Weak transcription	Brain Angular Gyrus	brain
38	chr7:2834600-2836600	Weak transcription	Brain Anterior Caudate	brain
39	chr7:2834600-2837400	Enhancers	Right Atrium	heart
40	chr7:2834600-2838800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr7:2834600-2840200	Weak transcription	Fetal Brain Female	brain
42	chr7:2834600-2840200	Weak transcription	Fetal Thymus	thymus
43	chr7:2834600-2840800	Weak transcription	Hela-S3	cervix
44	chr7:2834600-2840800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr7:2834600-2841000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:2834600-2841400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:2834600-2842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:2834600-2847800	Weak transcription	Liver	Liver
49	chr7:2834800-2836200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr7:2834800-2837200	Weak transcription	A549	lung

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