Variant report

Variant	rs1560064
Chromosome Location	chr5:5189203-5189204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10036706	0.81[JPT][hapmap]
rs10037656	0.91[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes]
rs10040074	0.80[AMR][1000 genomes]
rs11743270	0.83[CHD][hapmap]
rs4702241	0.83[CHD][hapmap];0.84[GIH][hapmap];0.81[ASN][1000 genomes]
rs871122	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021653	chr5:4932992-5201887	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers 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	nsv1024784	chr5:4980979-5391231	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1032719	chr5:5102763-5387406	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv537621	chr5:5102763-5387406	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1560064	MTRR	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5182000-5200400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:5183000-5192600	Weak transcription	HSMMtube	muscle
3	chr5:5183800-5189400	Weak transcription	Gastric	stomach
4	chr5:5184400-5190000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:5184600-5190000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:5184600-5204000	Weak transcription	Pancreas	Pancrea
7	chr5:5184800-5199200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:5185000-5199400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:5185200-5201200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:5185200-5262800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:5185400-5192000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:5185600-5199200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:5185800-5199400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:5186000-5199400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:5186000-5199800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr5:5186200-5190200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:5187200-5191200	Enhancers	Fetal Kidney	kidney
18	chr5:5187400-5190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:5187400-5192200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:5187400-5192200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:5187800-5189800	Strong transcription	NH-A	brain
22	chr5:5189200-5190000	Weak transcription	Ovary	ovary
23	chr5:5189200-5198400	Weak transcription	Fetal Muscle Leg	muscle

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