Variant report

Variant	rs7842882
Chromosome Location	chr8:125284385-125284386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125283455..125287567-chr8:125381773..125385340,3	MCF-7	breast:
2	chr8:125283962..125286170-chr8:125287924..125291020,4	MCF-7	breast:
3	chr8:125258129..125260887-chr8:125283574..125285765,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214803	Chromatin interaction
ENSG00000164983	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10087001	0.81[ASN][1000 genomes]
rs10087062	0.89[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10087137	0.92[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10087222	0.92[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10087374	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10089870	0.85[ASN][1000 genomes]
rs10091808	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10092616	0.88[CEU][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13439237	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13439439	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13439443	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs17295226	0.92[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17295548	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17360690	0.90[CHB][hapmap]
rs17360711	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs17360746	0.92[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17360788	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4360277	0.92[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs4374970	0.92[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs4504618	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4593526	0.92[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4871476	0.92[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4871477	0.92[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4871478	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4871480	0.92[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4871481	0.92[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4871482	0.92[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55784871	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55932688	0.90[ASN][1000 genomes]
rs55945711	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56068026	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56218959	0.80[ASN][1000 genomes]
rs56234976	0.88[ASN][1000 genomes]
rs56383080	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60167901	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60995425	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66467223	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66961607	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67153514	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67712436	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67815046	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68047305	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6983392	0.81[ASN][1000 genomes]
rs6984141	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6984458	0.91[EUR][1000 genomes]
rs6984642	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6984921	0.92[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6986310	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6988141	0.82[ASN][1000 genomes]
rs7003238	0.81[ASN][1000 genomes]
rs7003974	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7011052	0.92[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7011213	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7011528	0.92[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72719397	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73330303	0.88[ASN][1000 genomes]
rs73330304	0.88[ASN][1000 genomes]
rs73345158	0.81[ASN][1000 genomes]
rs73345172	0.82[ASN][1000 genomes]
rs73345176	0.81[ASN][1000 genomes]
rs73345185	0.88[ASN][1000 genomes]
rs9297691	0.90[CHB][hapmap]
rs9297693	0.92[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9643192	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9969472	0.92[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9969473	0.92[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9969475	0.92[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9969479	0.92[EUR][1000 genomes]
rs9969480	0.92[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9969624	0.92[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7842882	RP11-383J24.1	cis	Muscle Skeletal	GTEx
rs7842882	TRMT12	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125274800-125287400	Weak transcription	Fetal Brain Male	brain
2	chr8:125281200-125284400	Enhancers	Fetal Intestine Large	intestine
3	chr8:125281200-125284600	Enhancers	Psoas Muscle	Psoas
4	chr8:125281600-125285000	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr8:125282200-125284400	Enhancers	Fetal Intestine Small	intestine
6	chr8:125282200-125285600	Enhancers	NHDF-Ad	bronchial
7	chr8:125282400-125284600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr8:125282600-125284600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr8:125282800-125284400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:125282800-125284400	Enhancers	Left Ventricle	heart
11	chr8:125282800-125284400	Enhancers	HSMMtube	muscle
12	chr8:125282800-125284800	Enhancers	HUVEC	blood vessel
13	chr8:125282800-125285400	Flanking Active TSS	Hela-S3	cervix
14	chr8:125282800-125285400	Enhancers	NHLF	lung
15	chr8:125282800-125285600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr8:125283200-125284400	Enhancers	Colon Smooth Muscle	Colon
17	chr8:125283200-125285000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr8:125283200-125285600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:125283400-125284400	Enhancers	HMEC	breast
20	chr8:125283400-125284400	Enhancers	NHEK	skin
21	chr8:125283400-125284600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:125283400-125284600	Enhancers	HSMM	muscle
23	chr8:125283400-125285400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr8:125283600-125284400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr8:125283600-125284400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr8:125283600-125284400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr8:125283800-125284400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:125283800-125284400	Enhancers	HepG2	liver
29	chr8:125283800-125285000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr8:125284000-125284400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr8:125284000-125284400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr8:125284000-125284400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr8:125284000-125284400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr8:125284000-125284400	Enhancers	Pancreas	Pancrea
35	chr8:125284000-125284400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr8:125284000-125284400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr8:125284000-125284400	Flanking Active TSS	K562	blood
38	chr8:125284000-125284400	Flanking Active TSS	Osteobl	bone
39	chr8:125284000-125285000	Flanking Active TSS	NH-A	brain
40	chr8:125284000-125285200	Enhancers	Right Ventricle	heart
41	chr8:125284000-125285600	Flanking Active TSS	A549	lung
42	chr8:125284200-125284400	Enhancers	Right Atrium	heart
43	chr8:125284200-125285200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links