Variant report

Variant	rs28497053
Chromosome Location	chr15:51213529-51213530
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	chr15:51213388..51216180-chr15:51233537..51235564,2	MCF-7	breast:
2	chr15:51207605..51209547-chr15:51210912..51214832,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLDN-6	chr15:51213504-51214133	NONHSAT042445

Variant related genes	Relation type
ENSG00000081014	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12101376	1.00[AFR][1000 genomes]
rs12101535	1.00[AFR][1000 genomes]
rs12102250	1.00[AFR][1000 genomes]
rs28397739	1.00[AFR][1000 genomes]
rs28415694	1.00[AFR][1000 genomes]
rs28437695	1.00[AFR][1000 genomes]
rs28463775	1.00[AFR][1000 genomes]
rs28464432	1.00[AFR][1000 genomes]
rs28478740	1.00[AFR][1000 genomes]
rs28510866	1.00[AFR][1000 genomes]
rs28544375	1.00[AFR][1000 genomes]
rs28637248	1.00[AFR][1000 genomes]
rs28675179	1.00[AFR][1000 genomes]
rs28682435	1.00[AFR][1000 genomes]
rs28693451	1.00[AFR][1000 genomes]
rs28707532	1.00[AFR][1000 genomes]
rs28708725	1.00[AFR][1000 genomes]
rs28736316	1.00[AFR][1000 genomes]
rs28870167	1.00[AFR][1000 genomes]
rs28878017	1.00[AFR][1000 genomes]
rs9920041	1.00[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	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv516168	chr15:51114437-51217361	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51201600-51243200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:51201600-51245000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:51201800-51223200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:51201800-51230600	Weak transcription	K562	blood
5	chr15:51201800-51242800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr15:51201800-51248400	Weak transcription	Colonic Mucosa	Colon
7	chr15:51201800-51271600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:51202000-51217200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:51202000-51219000	Weak transcription	Right Ventricle	heart
10	chr15:51202200-51214200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:51202200-51222600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:51202400-51213600	Weak transcription	Brain Germinal Matrix	brain
13	chr15:51202600-51214200	Weak transcription	Esophagus	oesophagus
14	chr15:51202600-51236800	Weak transcription	Small Intestine	intestine
15	chr15:51202600-51241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:51202600-51242800	Weak transcription	Gastric	stomach
17	chr15:51202800-51218600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:51202800-51219200	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:51202800-51219400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:51202800-51230400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:51202800-51243400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:51203000-51221600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:51203000-51230400	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:51203200-51242200	Weak transcription	Brain Substantia Nigra	brain
25	chr15:51203200-51242800	Weak transcription	Lung	lung
26	chr15:51203400-51242400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr15:51203600-51214000	Weak transcription	NHLF	lung
28	chr15:51203800-51225800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:51204000-51231200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:51204200-51231200	Strong transcription	Placenta	Placenta
31	chr15:51204400-51215800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:51204600-51229000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:51204800-51225200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr15:51204800-51243000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:51205000-51226400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:51205400-51220200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:51205600-51242800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr15:51205800-51214000	Weak transcription	NHEK	skin
39	chr15:51205800-51214200	Weak transcription	Fetal Lung	lung
40	chr15:51205800-51249000	Weak transcription	Fetal Brain Male	brain
41	chr15:51205800-51254400	Weak transcription	Fetal Heart	heart
42	chr15:51206000-51221000	Weak transcription	HMEC	breast
43	chr15:51206600-51215000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:51206600-51219000	Weak transcription	HUVEC	blood vessel
45	chr15:51207000-51214200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:51207600-51215000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr15:51208000-51250400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:51208400-51242200	Weak transcription	Fetal Kidney	kidney
49	chr15:51209200-51215000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:51209200-51217000	Weak transcription	GM12878-XiMat	blood

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