Variant report

Variant	rs798512
Chromosome Location	chr7:2782592-2782593
allele	C/G
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: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11354	1.00[YRI][hapmap]
rs1182175	0.84[CEU][hapmap]
rs1182191	0.81[CEU][hapmap]
rs1182194	0.81[CEU][hapmap]
rs1182196	0.81[CEU][hapmap];0.93[JPT][hapmap]
rs1182197	0.84[CHB][hapmap]
rs1182198	0.91[JPT][hapmap]
rs1182207	0.84[ASN][1000 genomes]
rs1182208	0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1182209	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13243214	0.86[ASN][1000 genomes]
rs1713920	0.81[CEU][hapmap]
rs2107964	0.80[JPT][hapmap]
rs2158694	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2248390	0.80[ASN][1000 genomes]
rs2251491	0.80[ASN][1000 genomes]
rs2260230	0.85[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2266922	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283779	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2283783	0.80[ASN][1000 genomes]
rs2283784	0.80[ASN][1000 genomes]
rs2527683	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527684	0.88[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527687	0.84[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2527690	0.82[CEU][hapmap]
rs2527692	0.80[ASN][1000 genomes]
rs2644274	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2644275	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2644294	0.82[ASN][1000 genomes]
rs2644295	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2644296	0.84[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2644297	0.86[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap]
rs2644312	0.81[JPT][hapmap]
rs35957220	0.87[ASN][1000 genomes]
rs6970963	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6978692	0.80[ASN][1000 genomes]
rs709282	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs757787	0.84[AFR][1000 genomes]
rs757791	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs7777484	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7807978	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798480	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798481	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798482	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798485	0.89[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs798486	0.89[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs798487	0.90[ASN][1000 genomes]
rs798488	0.84[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs798490	0.84[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs798491	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs798492	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798493	0.94[ASN][1000 genomes]
rs798494	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs798495	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs798496	0.90[ASN][1000 genomes]
rs798497	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs798498	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs798499	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798500	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs798502	0.81[CHB][hapmap]
rs798503	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs798508	0.96[ASN][1000 genomes]
rs798511	0.96[ASN][1000 genomes]
rs798513	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798514	0.95[ASN][1000 genomes]
rs798518	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs798526	0.97[ASN][1000 genomes]
rs798528	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs798531	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs798536	0.87[ASN][1000 genomes]
rs798540	0.84[ASN][1000 genomes]
rs798544	0.89[ASN][1000 genomes]
rs798545	0.89[ASN][1000 genomes]
rs798546	0.89[ASN][1000 genomes]
rs798547	0.93[ASN][1000 genomes]
rs798548	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs798550	0.93[ASN][1000 genomes]
rs798551	0.93[ASN][1000 genomes]
rs798552	0.93[ASN][1000 genomes]
rs798554	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs798555	0.89[ASN][1000 genomes]
rs798556	0.95[CHB][hapmap];0.93[ASN][1000 genomes]
rs798557	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs798558	0.93[ASN][1000 genomes]
rs798559	0.86[ASN][1000 genomes]
rs798560	0.86[ASN][1000 genomes]
rs798562	0.88[ASN][1000 genomes]
rs798563	0.82[ASN][1000 genomes]
rs798565	0.82[CHB][hapmap]
rs960273	0.85[CHB][hapmap];0.86[JPT][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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs798512	GNA12	cis	Nerve Tibial	GTEx
rs798512	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs798512		cis	Lymphoblastoid	GTEx
rs798512	LOC392620	cis	multi-tissue	Pritchard
rs798512	GNA12	cis	multi-tissue	Pritchard

Chromatin state (count:69 , 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	chr7:2771200-2783200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:2771200-2796200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:2771400-2785000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:2771400-2796200	Weak transcription	NHEK	skin
8	chr7:2772800-2783200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:2773200-2783200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:2773200-2796200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:2773200-2796400	Weak transcription	NH-A	brain
12	chr7:2773200-2797000	Weak transcription	Pancreas	Pancrea
13	chr7:2773600-2796400	Weak transcription	Osteobl	bone
14	chr7:2775200-2783200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr7:2775200-2783200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:2775200-2790600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:2775200-2791600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:2775200-2796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:2775400-2789800	Weak transcription	Ovary	ovary
20	chr7:2775400-2790000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:2775400-2797400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr7:2775400-2801200	Weak transcription	Primary T cells from cord blood	blood
23	chr7:2775800-2796400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:2775800-2796400	Weak transcription	HSMM	muscle
25	chr7:2776200-2782800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:2776200-2797000	Weak transcription	Spleen	Spleen
27	chr7:2776400-2783400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:2776600-2784000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:2776800-2782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:2776800-2783200	Weak transcription	Fetal Intestine Large	intestine
31	chr7:2776800-2793600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:2776800-2796200	Weak transcription	HepG2	liver
33	chr7:2777600-2796200	Weak transcription	Dnd41	blood
34	chr7:2778200-2796400	Weak transcription	Psoas Muscle	Psoas
35	chr7:2778600-2790800	Weak transcription	Adipose Nuclei	Adipose
36	chr7:2778600-2794800	Weak transcription	Primary B cells from cord blood	blood
37	chr7:2778600-2796200	Weak transcription	Fetal Lung	lung
38	chr7:2778600-2796400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr7:2778800-2782600	Weak transcription	Right Atrium	heart
40	chr7:2778800-2782800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:2778800-2784400	Weak transcription	Fetal Muscle Leg	muscle
42	chr7:2778800-2789600	Weak transcription	K562	blood
43	chr7:2778800-2789800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr7:2778800-2795800	Weak transcription	Placenta	Placenta
45	chr7:2778800-2796200	Weak transcription	NHLF	lung
46	chr7:2779000-2784200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr7:2779000-2796600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr7:2779200-2783200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr7:2779400-2783400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:2779400-2789400	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links