Variant report

Variant	rs798489
Chromosome Location	chr7:2801803-2801804
allele	A/G
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	RAD21	chr7:2799243-2801814	SK-N-SH	brain:	n/a	chr7:2799554-2799564 chr7:2799556-2799570

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2801788..2804432-chr7:2882018..2884117,3	K562	blood:

Variant related genes	Relation type
GNA12	TF binding region
AMZ1	TF binding region
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1182174	0.90[CEU][hapmap]
rs1182177	0.91[CEU][hapmap]
rs1182179	0.91[CEU][hapmap]
rs1182181	0.91[CEU][hapmap]
rs1182183	0.86[CEU][hapmap]
rs1182185	0.90[CEU][hapmap]
rs1182187	0.81[EUR][1000 genomes]
rs1182188	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1182189	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1182198	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs1182207	0.91[EUR][1000 genomes]
rs1182208	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs13243214	0.89[EUR][1000 genomes]
rs1636264	0.86[CEU][hapmap]
rs1713919	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs2107964	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2158694	0.87[CEU][hapmap]
rs2260230	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2533878	0.91[CEU][hapmap]
rs2533879	0.82[EUR][1000 genomes]
rs2533882	0.81[EUR][1000 genomes]
rs2533884	0.86[EUR][1000 genomes]
rs2644294	0.85[EUR][1000 genomes]
rs2644312	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs35957220	0.90[EUR][1000 genomes]
rs798485	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs798486	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs798487	0.91[EUR][1000 genomes]
rs798488	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs798490	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs798491	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs798493	0.92[EUR][1000 genomes]
rs798494	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs798495	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs798496	0.80[EUR][1000 genomes]
rs798497	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs798498	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs798500	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs798502	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs798506	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs798508	0.83[EUR][1000 genomes]
rs798511	0.84[EUR][1000 genomes]
rs798514	0.83[EUR][1000 genomes]
rs798518	0.83[CEU][hapmap]
rs798526	0.81[EUR][1000 genomes]
rs798528	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs798548	0.82[CEU][hapmap]
rs960273	0.91[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
7	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:1)

Disease	PMID	Source
Height	20881960	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs798489	GNA12	cis	multi-tissue	Pritchard
rs798489	GNA12	cis	Nerve Tibial	GTEx
rs798489	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr7:2790000-2830400	Weak transcription	Aorta	Aorta
3	chr7:2791200-2803400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:2796400-2803200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr7:2796400-2804000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr7:2796800-2802000	Enhancers	Adipose Nuclei	Adipose
7	chr7:2796800-2803600	Weak transcription	Primary B cells from cord blood	blood
8	chr7:2796800-2804400	Enhancers	Fetal Muscle Leg	muscle
9	chr7:2797000-2803200	Enhancers	Right Ventricle	heart
10	chr7:2797000-2803800	Enhancers	Brain Cingulate Gyrus	brain
11	chr7:2797000-2805400	Enhancers	Placenta	Placenta
12	chr7:2797600-2831200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:2798000-2803600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr7:2798000-2827400	Weak transcription	Thymus	Thymus
15	chr7:2798200-2803200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:2798400-2802000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:2798400-2802200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:2798400-2802200	Enhancers	Osteobl	bone
19	chr7:2798400-2803000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:2798600-2802000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:2799000-2803800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr7:2799200-2802200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:2799200-2802400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr7:2799200-2802400	Enhancers	Right Atrium	heart
25	chr7:2799200-2802600	Enhancers	Left Ventricle	heart
26	chr7:2799200-2804400	Enhancers	Ovary	ovary
27	chr7:2799200-2804600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:2799200-2817000	Weak transcription	Dnd41	blood
29	chr7:2799200-2827200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:2799600-2802400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:2799600-2803800	Genic enhancers	Fetal Stomach	stomach
32	chr7:2799600-2807600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:2799600-2825600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:2800200-2802200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:2800200-2802400	Enhancers	Brain Anterior Caudate	brain
36	chr7:2800200-2803600	Enhancers	Fetal Heart	heart
37	chr7:2800200-2806400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:2800200-2815800	Weak transcription	Liver	Liver
39	chr7:2800400-2802000	Genic enhancers	NHLF	lung
40	chr7:2800400-2802200	Weak transcription	HMEC	breast
41	chr7:2800400-2804400	Enhancers	NHDF-Ad	bronchial
42	chr7:2800400-2810200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:2800600-2802000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr7:2800600-2802000	Enhancers	Rectal Smooth Muscle	rectum
45	chr7:2800600-2802000	Weak transcription	HUVEC	blood vessel
46	chr7:2800600-2802200	Weak transcription	NH-A	brain
47	chr7:2800600-2802400	Enhancers	Brain Hippocampus Middle	brain
48	chr7:2800600-2802800	Enhancers	Brain Substantia Nigra	brain
49	chr7:2800600-2802800	Weak transcription	Fetal Brain Female	brain
50	chr7:2800600-2803800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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