Variant report

Variant	rs1992112
Chromosome Location	chr5:59020054-59020055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58968638..58970043-chr5:59019689..59021106,4	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10061253	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1011644	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10514857	0.85[TSI][hapmap]
rs1370230	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs169869	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17742664	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164661	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs256356	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs2938784	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs2938785	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2963824	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap]
rs297974	0.83[EUR][1000 genomes]
rs298057	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs298058	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs298059	0.82[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs298061	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs298062	0.81[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.84[ASN][1000 genomes]
rs298063	0.82[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs298067	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs298072	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs298074	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs298075	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs298076	0.89[EUR][1000 genomes]
rs298082	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs298083	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs298084	0.82[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs298091	0.82[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs298092	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs298093	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs298096	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs298097	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs298100	0.89[YRI][hapmap]
rs402874	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4235477	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs6450526	0.82[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6450527	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6450529	0.98[ASN][1000 genomes]
rs6450531	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs6450532	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs6865459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6869459	0.95[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs6875753	0.90[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs7701573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720119	0.85[LWK][hapmap];0.89[YRI][hapmap]
rs905834	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs981230	0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv462190	chr5:58936943-59023870	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv598258	chr5:58936943-59023870	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1034283	chr5:58940594-59040762	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv537767	chr5:58940594-59040762	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv462191	chr5:58993297-59038610	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv598259	chr5:58993297-59038610	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1992112	PTPRG	trans	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59009800-59023400	Weak transcription	Fetal Lung	lung
2	chr5:59011200-59020400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:59011200-59020600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:59012400-59021000	Weak transcription	Gastric	stomach
5	chr5:59013800-59021000	Weak transcription	Fetal Brain Male	brain
6	chr5:59014400-59020800	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:59017800-59028400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:59018000-59021000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr5:59018000-59021400	Enhancers	A549	lung
10	chr5:59018200-59023600	Weak transcription	Brain Germinal Matrix	brain
11	chr5:59018400-59020200	Enhancers	Hela-S3	cervix
12	chr5:59018400-59020400	Enhancers	HUVEC	blood vessel
13	chr5:59018400-59021000	Enhancers	NHEK	skin
14	chr5:59018400-59021200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:59018600-59020200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:59018600-59020200	Enhancers	HMEC	breast
17	chr5:59018800-59021800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:59019000-59020800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:59019200-59021000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:59019400-59020600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr5:59019800-59020400	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr5:59019800-59020800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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