Variant report

Variant	rs7998781
Chromosome Location	chr13:49138910-49138911
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	chr13:49106089..49108573-chr13:49138293..49140212,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136161	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1547660	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1926595	0.96[ASN][1000 genomes]
rs1926596	0.88[ASN][1000 genomes]
rs1926597	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs198564	0.82[ASN][1000 genomes]
rs198568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs198606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs198610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2274400	0.88[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs28414460	0.88[ASN][1000 genomes]
rs2854357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2854362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28646083	0.88[ASN][1000 genomes]
rs28674973	0.81[ASN][1000 genomes]
rs2897587	0.90[AFR][1000 genomes]
rs3092888	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3092898	0.85[ASN][1000 genomes]
rs3751380	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs398158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs403390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs406098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4151525	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs4151601	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs425834	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs427686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61074776	0.96[ASN][1000 genomes]
rs6561448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6561457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6561461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6561465	1.00[CEU][hapmap]
rs7325962	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs7326934	0.89[YRI][hapmap]
rs7329039	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7329865	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs73486867	0.96[ASN][1000 genomes]
rs73495016	0.85[ASN][1000 genomes]
rs7985825	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7987935	0.88[ASN][1000 genomes]
rs7992129	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7995216	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7996186	0.88[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7996402	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8001241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8002565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316385	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9316401	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9331959	0.88[ASN][1000 genomes]
rs9331965	0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9331973	0.88[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9332054	0.90[JPT][hapmap]
rs9591172	0.96[ASN][1000 genomes]
rs9591177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9591178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9595929	0.88[AFR][1000 genomes]
rs9595931	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49135000-49140000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr13:49135000-49155000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr13:49135200-49141800	Weak transcription	Placenta	Placenta
4	chr13:49136800-49141200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr13:49136800-49141400	Weak transcription	HepG2	liver
6	chr13:49136800-49142000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:49137000-49139000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr13:49137000-49139600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:49137000-49141600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:49137000-49142000	Weak transcription	HMEC	breast
11	chr13:49137200-49139200	Enhancers	Dnd41	blood
12	chr13:49137200-49139400	Enhancers	GM12878-XiMat	blood
13	chr13:49137200-49141400	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr13:49137200-49141600	Weak transcription	HSMM	muscle
15	chr13:49137200-49153000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr13:49137400-49145200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr13:49137600-49140000	Enhancers	K562	blood
18	chr13:49137800-49139600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr13:49137800-49140600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr13:49138200-49139800	Enhancers	Fetal Lung	lung
21	chr13:49138600-49139000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:49138600-49141000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr13:49138600-49141200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr13:49138600-49141400	Weak transcription	HSMMtube	muscle
25	chr13:49138600-49141600	Weak transcription	Osteobl	bone
26	chr13:49138600-49142000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:49138800-49140800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:49138800-49141400	Weak transcription	Stomach Mucosa	stomach
29	chr13:49138800-49145600	Weak transcription	HUVEC	blood vessel

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