Variant report

Variant	rs6725080
Chromosome Location	chr2:86725067-86725068
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	chr2:86720517..86722121-chr2:86723212..86725706,2	K562	blood:
2	chr2:86720341..86722407-chr2:86724543..86726613,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1015117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10180036	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs10184879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap]
rs10187880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1020306	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11127045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11127046	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11127047	0.83[CHD][hapmap];0.81[GIH][hapmap]
rs1137684	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676576	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11684230	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11689330	0.80[AFR][1000 genomes]
rs12613282	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap]
rs12614447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12623509	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap]
rs12714184	0.83[EUR][1000 genomes]
rs12714186	1.00[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs12714188	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12714190	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs12714198	0.86[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap]
rs12714199	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12987172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs13015620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs13034615	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13390713	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13408041	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13429696	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1465813	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1518807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1629293	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap]
rs2241803	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292887	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2367574	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088046	0.81[ASN][1000 genomes]
rs308902	0.91[GIH][hapmap]
rs308903	0.89[GIH][hapmap]
rs308910	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs308914	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs308915	0.87[GIH][hapmap]
rs3201448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731812	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770058	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422240	0.90[CHD][hapmap];0.93[GIH][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs4832040	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832296	0.83[ASN][1000 genomes]
rs4832297	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4832300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs4832304	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs62150269	0.81[EUR][1000 genomes]
rs6738663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs6750226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs6752371	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs7369138	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7557796	0.88[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap]
rs7568840	0.88[CHB][hapmap]
rs7584882	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap]
rs7593151	0.83[ASN][1000 genomes]
rs7596717	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs8179729	0.83[ASN][1000 genomes]
rs9284788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs958561	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9789777	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6725080	RNF103	cis	cerebellum	SCAN
rs6725080	IMMT	cis	cerebellum	SCAN
rs6725080	POLR1A	cis	cerebellum	SCAN
rs6725080	MAT2A	cis	parietal	SCAN
rs6725080	VPS24	cis	parietal	SCAN
rs6725080	PTCD3	cis	cerebellum	SCAN
rs6725080	C2orf68	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86671000-86725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:86671400-86725600	Strong transcription	A549	lung
3	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung
11	chr2:86684000-86726000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:86697800-86728800	Strong transcription	Primary T cells from cord blood	blood
15	chr2:86699400-86727000	Strong transcription	Placenta	Placenta
16	chr2:86701000-86725600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:86704800-86726400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:86704800-86726600	Strong transcription	NHDF-Ad	bronchial
19	chr2:86708800-86726600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:86709200-86726600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:86709800-86725600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:86712800-86726600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:86713400-86727400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:86716600-86725200	Weak transcription	Aorta	Aorta
26	chr2:86717200-86726600	Weak transcription	Pancreas	Pancrea
27	chr2:86717400-86726600	Weak transcription	Stomach Mucosa	stomach
28	chr2:86718600-86725200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:86718800-86726600	Weak transcription	Gastric	stomach
30	chr2:86718800-86726600	Weak transcription	Right Ventricle	heart
31	chr2:86719400-86725200	Weak transcription	NHEK	skin
32	chr2:86719400-86726000	Strong transcription	HSMM	muscle
33	chr2:86719400-86726600	Weak transcription	Spleen	Spleen
34	chr2:86719800-86725200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:86719800-86725400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr2:86719800-86725400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:86719800-86725400	Weak transcription	K562	blood
38	chr2:86719800-86726600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:86719800-86726800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:86719800-86726800	Strong transcription	Liver	Liver
41	chr2:86719800-86726800	Weak transcription	Esophagus	oesophagus
42	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
43	chr2:86720000-86725400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:86720000-86725400	Weak transcription	HSMMtube	muscle
45	chr2:86720200-86725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:86720200-86725600	Weak transcription	Fetal Heart	heart
47	chr2:86720400-86726600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr2:86720400-86727000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:86720600-86725800	Weak transcription	Hela-S3	cervix
50	chr2:86720600-86726000	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links