Variant report

Variant	rs6719375
Chromosome Location	chr2:63521424-63521425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63519650..63522564-chr2:63524374..63526614,2	MCF-7	breast:
2	chr2:63519666..63522078-chr2:63524666..63526969,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10173637	0.86[EUR][1000 genomes]
rs10201254	0.85[EUR][1000 genomes]
rs10207356	0.81[EUR][1000 genomes]
rs11125957	0.87[EUR][1000 genomes]
rs11675647	0.81[EUR][1000 genomes]
rs11684108	0.82[EUR][1000 genomes]
rs11685910	0.85[EUR][1000 genomes]
rs11691166	0.86[EUR][1000 genomes]
rs11691718	0.82[EUR][1000 genomes]
rs12612773	0.81[EUR][1000 genomes]
rs12623431	0.82[EUR][1000 genomes]
rs12713476	0.87[EUR][1000 genomes]
rs12713477	0.82[EUR][1000 genomes]
rs12713478	0.81[EUR][1000 genomes]
rs12994711	0.82[EUR][1000 genomes]
rs13020171	0.86[EUR][1000 genomes]
rs13387839	0.82[EUR][1000 genomes]
rs1400686	0.81[EUR][1000 genomes]
rs1400687	0.81[EUR][1000 genomes]
rs1400688	0.81[EUR][1000 genomes]
rs1517401	0.81[EUR][1000 genomes]
rs1517402	0.81[EUR][1000 genomes]
rs1517404	0.81[EUR][1000 genomes]
rs1517405	0.82[EUR][1000 genomes]
rs1589092	0.85[EUR][1000 genomes]
rs1607203	0.85[EUR][1000 genomes]
rs1607204	0.85[EUR][1000 genomes]
rs1607205	0.85[EUR][1000 genomes]
rs2030188	0.81[EUR][1000 genomes]
rs2030189	0.80[EUR][1000 genomes]
rs2030190	0.81[EUR][1000 genomes]
rs2090478	0.80[EUR][1000 genomes]
rs2090479	0.81[EUR][1000 genomes]
rs2263636	0.82[EUR][1000 genomes]
rs2421881	0.86[EUR][1000 genomes]
rs2421884	0.87[EUR][1000 genomes]
rs2464042	0.85[EUR][1000 genomes]
rs2677436	0.84[EUR][1000 genomes]
rs2677437	0.85[EUR][1000 genomes]
rs2677438	0.85[EUR][1000 genomes]
rs2677442	0.84[EUR][1000 genomes]
rs2699388	0.85[EUR][1000 genomes]
rs2699389	0.85[EUR][1000 genomes]
rs2699390	0.85[EUR][1000 genomes]
rs2699391	0.85[EUR][1000 genomes]
rs2699399	0.85[EUR][1000 genomes]
rs2945032	0.85[EUR][1000 genomes]
rs2951185	0.84[EUR][1000 genomes]
rs2951186	0.85[EUR][1000 genomes]
rs2951192	0.85[EUR][1000 genomes]
rs4416201	0.87[EUR][1000 genomes]
rs4428008	0.87[EUR][1000 genomes]
rs4560098	0.86[EUR][1000 genomes]
rs4602212	0.82[EUR][1000 genomes]
rs4611627	0.86[EUR][1000 genomes]
rs4632325	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4671468	0.86[EUR][1000 genomes]
rs4671469	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4671470	0.81[EUR][1000 genomes]
rs4671471	0.82[EUR][1000 genomes]
rs4671472	0.82[EUR][1000 genomes]
rs4671473	0.81[EUR][1000 genomes]
rs4671474	0.82[EUR][1000 genomes]
rs4671475	0.82[EUR][1000 genomes]
rs4671476	0.82[EUR][1000 genomes]
rs4671478	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671479	0.81[EUR][1000 genomes]
rs4671480	0.81[EUR][1000 genomes]
rs4671481	0.81[EUR][1000 genomes]
rs62177793	0.81[EUR][1000 genomes]
rs62177797	0.81[EUR][1000 genomes]
rs62177820	0.81[EUR][1000 genomes]
rs62177821	0.81[EUR][1000 genomes]
rs62177824	0.85[EUR][1000 genomes]
rs6545984	0.87[EUR][1000 genomes]
rs6545985	0.87[EUR][1000 genomes]
rs6545986	0.82[EUR][1000 genomes]
rs6545988	0.84[EUR][1000 genomes]
rs6545989	0.81[EUR][1000 genomes]
rs6704562	0.81[EUR][1000 genomes]
rs6705776	0.87[EUR][1000 genomes]
rs6706180	0.82[EUR][1000 genomes]
rs6706424	0.82[EUR][1000 genomes]
rs6708627	0.81[EUR][1000 genomes]
rs6708847	0.82[EUR][1000 genomes]
rs6709115	0.81[EUR][1000 genomes]
rs6713500	0.81[EUR][1000 genomes]
rs6714298	0.82[EUR][1000 genomes]
rs6724044	0.82[EUR][1000 genomes]
rs6725694	0.82[EUR][1000 genomes]
rs6729132	0.82[EUR][1000 genomes]
rs6734468	0.82[EUR][1000 genomes]
rs6737820	0.81[EUR][1000 genomes]
rs6744720	0.82[EUR][1000 genomes]
rs6755183	0.82[EUR][1000 genomes]
rs6755412	0.81[EUR][1000 genomes]
rs7349440	0.85[EUR][1000 genomes]
rs7570649	0.81[EUR][1000 genomes]
rs7585664	0.82[EUR][1000 genomes]
rs7591562	0.82[EUR][1000 genomes]
rs7596446	0.86[EUR][1000 genomes]
rs7596580	0.84[EUR][1000 genomes]
rs7605113	0.81[EUR][1000 genomes]
rs7608966	0.87[EUR][1000 genomes]
rs9967684	0.87[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	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1004678	chr2:63230722-63562484	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv535768	chr2:63413596-63631407	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1009191	chr2:63473443-63578508	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv834241	chr2:63490262-63668205	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6719375	MDH1	cis	Adipose Subcutaneous	GTEx
rs6719375	WDPCP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63515400-63526200	Weak transcription	Gastric	stomach
2	chr2:63518200-63524600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:63520200-63524200	Weak transcription	Ovary	ovary
4	chr2:63520400-63525200	Weak transcription	Pancreas	Pancrea

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