Variant report

Variant	rs13339951
Chromosome Location	chr21:45007956-45007957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45006194..45009142-chr21:45021772..45023850,3	MCF-7	breast:
2	chr21:44931738..44933957-chr21:45005070..45008681,4	MCF-7	breast:
3	chr21:44940715..44942547-chr21:45006167..45008707,3	MCF-7	breast:
4	chr21:44595418..44598407-chr21:45007465..45009708,2	MCF-7	breast:
5	chr21:45006048..45008566-chr21:45024329..45026628,2	MCF-7	breast:
6	chr21:45000029..45003162-chr21:45004279..45008488,5	MCF-7	breast:
7	chr21:45005141..45010452-chr21:45028185..45033118,8	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10483077	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11089065	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11908893	1.00[MEX][hapmap]
rs11908919	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11909195	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11909530	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11909813	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11909999	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11910220	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11910351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11910352	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11911293	0.83[AFR][1000 genomes]
rs11911483	0.88[AFR][1000 genomes]
rs11911560	1.00[MEX][hapmap]
rs11911735	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11911856	0.82[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12106371	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12106423	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12106466	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12626631	0.92[YRI][hapmap]
rs17004507	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004572	0.85[YRI][hapmap]
rs17004580	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004581	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004582	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004585	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004586	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004587	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004589	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004590	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004596	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap]
rs17004600	1.00[MEX][hapmap]
rs17004602	1.00[MEX][hapmap]
rs2117981	1.00[MEX][hapmap];0.92[YRI][hapmap]
rs59298188	0.93[AMR][1000 genomes]
rs6381	1.00[MEX][hapmap]
rs7283618	0.93[AFR][1000 genomes]

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	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv1061539	chr21:44915533-45041824	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1067171	chr21:44921187-45039471	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv521700	chr21:44925334-45041790	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	nsv470903	chr21:44925334-45061501	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	nsv459289	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
7	nsv587690	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1065359	chr21:44967209-45029878	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv3537	chr21:44967340-45013104	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv834106	chr21:44992387-45109489	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv587700	chr21:45007956-45095200	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44995000-45024200	Weak transcription	Fetal Brain Male	brain
2	chr21:45004600-45014200	Enhancers	HepG2	liver
3	chr21:45005000-45008000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr21:45005000-45008000	Enhancers	HSMM	muscle
5	chr21:45005000-45011800	Enhancers	HMEC	breast
6	chr21:45005200-45008000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr21:45005200-45008200	Enhancers	HSMMtube	muscle
8	chr21:45005400-45008000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr21:45005400-45011800	Enhancers	Fetal Intestine Small	intestine
10	chr21:45005600-45010400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr21:45006000-45008600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:45006000-45008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr21:45006000-45010400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr21:45006000-45010400	Enhancers	Fetal Intestine Large	intestine
15	chr21:45006000-45011200	Weak transcription	Psoas Muscle	Psoas
16	chr21:45006000-45012600	Weak transcription	Ovary	ovary
17	chr21:45006200-45008800	Weak transcription	Placenta	Placenta
18	chr21:45006200-45008800	Weak transcription	Pancreas	Pancrea
19	chr21:45006200-45011600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr21:45006200-45012000	Weak transcription	Fetal Muscle Leg	muscle
21	chr21:45006200-45023000	Weak transcription	Right Atrium	heart
22	chr21:45006200-45024000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr21:45006400-45008600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr21:45006400-45008600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr21:45006400-45013400	Enhancers	Hela-S3	cervix
26	chr21:45006600-45008600	Weak transcription	Stomach Mucosa	stomach
27	chr21:45006600-45008800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr21:45006600-45010200	Weak transcription	NHDF-Ad	bronchial
29	chr21:45006600-45015200	Enhancers	A549	lung
30	chr21:45006800-45008600	Weak transcription	Small Intestine	intestine
31	chr21:45006800-45008800	Weak transcription	Osteobl	bone
32	chr21:45006800-45010200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr21:45006800-45010200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr21:45006800-45010600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr21:45006800-45010800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr21:45006800-45012800	Weak transcription	Adipose Nuclei	Adipose
37	chr21:45007000-45010200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr21:45007000-45016400	Weak transcription	NHLF	lung
39	chr21:45007200-45008600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr21:45007200-45009600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr21:45007200-45010600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr21:45007200-45011200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr21:45007400-45010000	Weak transcription	HUVEC	blood vessel
44	chr21:45007600-45008600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr21:45007800-45008600	Weak transcription	NHEK	skin
46	chr21:45007800-45009800	Weak transcription	NH-A	brain

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