Variant report

Variant	rs965913
Chromosome Location	chr5:50116456-50116457
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	chr5:50115536..50118140-chr5:50118384..50120343,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10461602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12654246	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12656298	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12656370	0.87[EUR][1000 genomes]
rs16877040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16884855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16884926	0.93[EUR][1000 genomes]
rs16885251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs27265	0.84[ASN][1000 genomes]
rs27828	0.84[ASN][1000 genomes]
rs4590146	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs55868205	0.87[EUR][1000 genomes]
rs58225490	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72753758	0.95[EUR][1000 genomes]
rs72753773	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72756138	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72756146	0.89[EUR][1000 genomes]
rs72756164	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7705385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7708414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:50064000-50126800	Weak transcription	Osteobl	bone
3	chr5:50071600-50138200	Weak transcription	Placenta	Placenta
4	chr5:50078200-50140000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:50083200-50116800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:50085400-50123800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:50085400-50136200	Weak transcription	Thymus	Thymus
8	chr5:50091200-50118800	Weak transcription	Spleen	Spleen
9	chr5:50091200-50123800	Weak transcription	Fetal Thymus	thymus
10	chr5:50091200-50124800	Weak transcription	Esophagus	oesophagus
11	chr5:50091200-50130400	Weak transcription	Pancreas	Pancrea
12	chr5:50091200-50133600	Weak transcription	Lung	lung
13	chr5:50091200-50136000	Weak transcription	Gastric	stomach
14	chr5:50091200-50140600	Weak transcription	Small Intestine	intestine
15	chr5:50091400-50124000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:50091800-50123400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:50094000-50123800	Weak transcription	HMEC	breast
18	chr5:50095800-50123400	Weak transcription	Fetal Lung	lung
19	chr5:50096000-50132200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:50099400-50123800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:50100000-50118600	Weak transcription	Aorta	Aorta
22	chr5:50100200-50139400	Weak transcription	Ovary	ovary
23	chr5:50100400-50116800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:50100400-50118800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr5:50100400-50123800	Weak transcription	Left Ventricle	heart
26	chr5:50102400-50118400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:50104600-50129400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:50104600-50136200	Weak transcription	NHEK	skin
29	chr5:50104800-50123600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:50107800-50118800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:50108000-50135000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:50108200-50142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:50109400-50124000	Weak transcription	Fetal Intestine Large	intestine
34	chr5:50109400-50141800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr5:50109600-50129000	Strong transcription	Dnd41	blood
36	chr5:50109800-50134400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:50109800-50136400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr5:50110000-50141800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr5:50110200-50118000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:50110400-50128000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
41	chr5:50110400-50133400	Strong transcription	Primary B cells from cord blood	blood
42	chr5:50110400-50143400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr5:50110400-50143600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:50110600-50134600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:50110800-50132000	Weak transcription	Brain Substantia Nigra	brain
46	chr5:50110800-50133400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:50110800-50140200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr5:50111000-50140800	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr5:50111200-50121000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr5:50111200-50141600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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