Variant report

Variant	rs798502
Chromosome Location	chr7:2789880-2789881
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2788053..2792290-chr7:2793052..2798708,8	K562	blood:
2	chr7:2777523..2779993-chr7:2788582..2791308,2	MCF-7	breast:
3	chr7:2788942..2791836-chr7:2793364..2795418,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1182155	0.81[TSI][hapmap]
rs1182174	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs1182176	0.81[EUR][1000 genomes]
rs1182177	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1182178	0.81[EUR][1000 genomes]
rs1182179	0.91[CEU][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs1182181	0.91[CEU][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs1182182	0.81[EUR][1000 genomes]
rs1182183	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs1182184	0.81[EUR][1000 genomes]
rs1182185	0.90[CEU][hapmap]
rs1182186	0.81[EUR][1000 genomes]
rs1182187	0.83[EUR][1000 genomes]
rs1182188	0.91[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1182189	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1182198	0.86[CEU][hapmap]
rs1182207	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1182208	0.94[CEU][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1183085	0.81[EUR][1000 genomes]
rs13243214	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1636249	0.81[TSI][hapmap]
rs1636250	0.84[ASW][hapmap];0.81[TSI][hapmap]
rs1636255	0.84[ASW][hapmap];0.94[TSI][hapmap]
rs1636264	0.86[CEU][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs1713919	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2107964	0.82[CEU][hapmap]
rs2158694	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2260230	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2533870	0.81[TSI][hapmap]
rs2533878	1.00[ASW][hapmap];0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2533879	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2533882	0.83[EUR][1000 genomes]
rs2533884	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644281	0.81[TSI][hapmap]
rs2644294	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2644312	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs35957220	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7783400	0.81[TSI][hapmap]
rs798485	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs798486	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs798487	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs798488	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs798489	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs798490	0.91[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs798491	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs798493	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs798494	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs798495	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798496	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs798497	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs798498	0.91[CEU][hapmap];0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs798499	0.81[CHB][hapmap]
rs798500	0.95[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs798503	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs798506	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798508	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs798511	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs798512	0.81[CHB][hapmap]
rs798514	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs798518	0.91[CEU][hapmap];0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs798526	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs798528	0.87[CEU][hapmap];0.81[CHB][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs798536	0.83[EUR][1000 genomes]
rs798540	0.81[EUR][1000 genomes]
rs798545	0.81[EUR][1000 genomes]
rs798546	0.82[EUR][1000 genomes]
rs798548	0.82[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap]
rs798550	0.81[EUR][1000 genomes]
rs798552	0.81[EUR][1000 genomes]
rs798554	0.86[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs798555	0.81[EUR][1000 genomes]
rs798556	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs798557	0.81[EUR][1000 genomes]
rs798558	0.81[EUR][1000 genomes]
rs798559	0.81[EUR][1000 genomes]
rs798565	0.81[AMR][1000 genomes]
rs960273	0.91[CEU][hapmap];0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv1032282	chr7:2789555-2820774	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	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

Variant related diseases (count:2)

Disease	PMID	Source
Ulcerative colitis	21297633	GWAS catalog
Ulcerative colitis	23128233	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs798502	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs798502	C7orf27	cis	parietal	SCAN
rs798502	GNA12	cis	multi-tissue	Pritchard
rs798502	GNA12	cis	Artery Tibial	GTEx
rs798502	GNA12	cis	lymphoblastoid	seeQTL
rs798502	GNA12	cis	Nerve Tibial	GTEx

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	chr7:2771200-2796200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:2771400-2796200	Weak transcription	NHEK	skin
6	chr7:2773200-2796200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:2773200-2796400	Weak transcription	NH-A	brain
8	chr7:2773200-2797000	Weak transcription	Pancreas	Pancrea
9	chr7:2773600-2796400	Weak transcription	Osteobl	bone
10	chr7:2775200-2790600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:2775200-2791600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:2775200-2796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:2775400-2790000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:2775400-2797400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:2775400-2801200	Weak transcription	Primary T cells from cord blood	blood
16	chr7:2775800-2796400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:2775800-2796400	Weak transcription	HSMM	muscle
18	chr7:2776200-2797000	Weak transcription	Spleen	Spleen
19	chr7:2776800-2793600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:2776800-2796200	Weak transcription	HepG2	liver
21	chr7:2777600-2796200	Weak transcription	Dnd41	blood
22	chr7:2778200-2796400	Weak transcription	Psoas Muscle	Psoas
23	chr7:2778600-2790800	Weak transcription	Adipose Nuclei	Adipose
24	chr7:2778600-2794800	Weak transcription	Primary B cells from cord blood	blood
25	chr7:2778600-2796200	Weak transcription	Fetal Lung	lung
26	chr7:2778600-2796400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:2778800-2795800	Weak transcription	Placenta	Placenta
28	chr7:2778800-2796200	Weak transcription	NHLF	lung
29	chr7:2779000-2796600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr7:2779400-2790400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr7:2779600-2796000	Weak transcription	Fetal Intestine Small	intestine
32	chr7:2780200-2796200	Weak transcription	Fetal Stomach	stomach
33	chr7:2782800-2797000	Weak transcription	Right Ventricle	heart
34	chr7:2782800-2797200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr7:2783000-2795600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr7:2783000-2798000	Weak transcription	Lung	lung
37	chr7:2783600-2796800	Weak transcription	Fetal Intestine Large	intestine
38	chr7:2783800-2790000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:2783800-2790600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:2783800-2797200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr7:2787400-2796200	Weak transcription	HSMMtube	muscle
42	chr7:2788400-2797400	Weak transcription	Thymus	Thymus
43	chr7:2789000-2790600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:2789400-2790000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr7:2789400-2790000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr7:2789400-2790200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:2789400-2790600	Enhancers	Fetal Heart	heart
49	chr7:2789600-2790000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:2789600-2790200	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links