Variant report

Variant	rs798509
Chromosome Location	chr7:2783428-2783429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2772073..2775942-chr7:2781505..2783799,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1182206	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs208346	0.96[ASN][1000 genomes]
rs208356	0.98[ASN][1000 genomes]
rs2251718	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2255541	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2255782	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2258960	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2266923	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2527682	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2527689	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2644272	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2644276	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644311	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2693566	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3846992	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs709280	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs709281	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs757789	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs757790	0.83[ASN][1000 genomes]
rs798501	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798504	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs798505	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs798515	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798516	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798517	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798519	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798520	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798521	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798522	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798523	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798524	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798525	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798527	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798529	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798530	0.87[EUR][1000 genomes];0.95[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	nsv1024023	chr7:2726210-2829581	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538653	chr7:2726210-2829581	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	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
6	nsv966746	chr7:2781545-2797621	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs798509	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs798509	GNA12	cis	Artery Tibial	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2752400-2796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:2761000-2796200	Weak transcription	Hela-S3	cervix
3	chr7:2761000-2797000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr7:2771200-2796200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:2771400-2785000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:2771400-2796200	Weak transcription	NHEK	skin
7	chr7:2773200-2796200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:2773200-2796400	Weak transcription	NH-A	brain
9	chr7:2773200-2797000	Weak transcription	Pancreas	Pancrea
10	chr7:2773600-2796400	Weak transcription	Osteobl	bone
11	chr7:2775200-2790600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:2775200-2791600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:2775200-2796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:2775400-2789800	Weak transcription	Ovary	ovary
15	chr7:2775400-2790000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:2775400-2797400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:2775400-2801200	Weak transcription	Primary T cells from cord blood	blood
18	chr7:2775800-2796400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:2775800-2796400	Weak transcription	HSMM	muscle
20	chr7:2776200-2797000	Weak transcription	Spleen	Spleen
21	chr7:2776600-2784000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:2776800-2793600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:2776800-2796200	Weak transcription	HepG2	liver
24	chr7:2777600-2796200	Weak transcription	Dnd41	blood
25	chr7:2778200-2796400	Weak transcription	Psoas Muscle	Psoas
26	chr7:2778600-2790800	Weak transcription	Adipose Nuclei	Adipose
27	chr7:2778600-2794800	Weak transcription	Primary B cells from cord blood	blood
28	chr7:2778600-2796200	Weak transcription	Fetal Lung	lung
29	chr7:2778600-2796400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:2778800-2784400	Weak transcription	Fetal Muscle Leg	muscle
31	chr7:2778800-2789600	Weak transcription	K562	blood
32	chr7:2778800-2789800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:2778800-2795800	Weak transcription	Placenta	Placenta
34	chr7:2778800-2796200	Weak transcription	NHLF	lung
35	chr7:2779000-2784200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr7:2779000-2796600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr7:2779400-2789400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr7:2779400-2789600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:2779400-2790400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:2779600-2796000	Weak transcription	Fetal Intestine Small	intestine
41	chr7:2780200-2789800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr7:2780200-2796200	Weak transcription	Fetal Stomach	stomach
43	chr7:2781600-2789800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:2782000-2783600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:2782000-2783600	Enhancers	Left Ventricle	heart
46	chr7:2782800-2797000	Weak transcription	Right Ventricle	heart
47	chr7:2782800-2797200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr7:2783000-2789600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:2783000-2795600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr7:2783000-2798000	Weak transcription	Lung	lung

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