Variant report

Variant	rs59896935
Chromosome Location	chr12:48524794-48524795
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48512350..48514595-chr12:48524789..48526462,2	MCF-7	breast:
2	chr12:48518519..48521118-chr12:48522824..48524892,2	MCF-7	breast:
3	chr12:48523386..48526206-chr12:48526341..48529296,3	K562	blood:
4	chr12:48524259..48525822-chr12:48531923..48533830,2	MCF-7	breast:
5	chr12:48515142..48518168-chr12:48522729..48524957,3	MCF-7	breast:
6	chr12:48518849..48522822-chr12:48523598..48527122,4	K562	blood:
7	chr12:48511904..48514441-chr12:48524039..48526074,2	MCF-7	breast:
8	chr12:48524575..48527145-chr12:48529433..48531470,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs55759881	0.83[AMR][1000 genomes]
rs55789595	0.83[AMR][1000 genomes]
rs55991805	1.00[AMR][1000 genomes]
rs56009798	0.83[AFR][1000 genomes]
rs56692411	0.83[AFR][1000 genomes]
rs57539024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58148022	0.83[AMR][1000 genomes]
rs58373242	0.83[AMR][1000 genomes]
rs59051221	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59233899	0.90[AFR][1000 genomes]
rs59643562	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59787033	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60001451	1.00[AMR][1000 genomes]
rs60316794	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60432008	0.86[AFR][1000 genomes]
rs61558457	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61750873	0.83[AMR][1000 genomes]
rs7316275	1.00[AMR][1000 genomes]
rs74086781	0.83[AMR][1000 genomes]
rs74086968	0.83[AMR][1000 genomes]
rs74086984	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74086997	0.83[AFR][1000 genomes]
rs74089112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089120	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089122	0.83[AFR][1000 genomes]
rs74089127	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089135	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089149	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089151	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089154	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089161	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089171	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089540	0.83[AMR][1000 genomes]
rs74089548	0.83[AMR][1000 genomes]
rs74089549	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48513400-48524800	Weak transcription	Liver	Liver
2	chr12:48513400-48526600	Weak transcription	Spleen	Spleen
3	chr12:48513600-48526400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:48513600-48527000	Weak transcription	Pancreas	Pancrea
5	chr12:48513800-48525000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:48513800-48525000	Weak transcription	Lung	lung
7	chr12:48513800-48525800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:48513800-48526000	Weak transcription	Colonic Mucosa	Colon
9	chr12:48513800-48526400	Weak transcription	Gastric	stomach
10	chr12:48513800-48526600	Weak transcription	Thymus	Thymus
11	chr12:48513800-48526800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:48514000-48525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:48514000-48525000	Weak transcription	Brain Substantia Nigra	brain
14	chr12:48514000-48525000	Weak transcription	Esophagus	oesophagus
15	chr12:48514000-48525600	Weak transcription	Placenta	Placenta
16	chr12:48514000-48526400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:48514000-48526600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:48514000-48526600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:48514200-48527000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:48514400-48525400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:48514400-48526400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:48514600-48526200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:48514800-48526000	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:48515800-48535600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:48515800-48545600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:48516200-48529600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:48516200-48545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:48516400-48529400	Strong transcription	Ovary	ovary
33	chr12:48516400-48529600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:48516400-48535600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:48516400-48535800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:48516400-48542000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:48516400-48545000	Strong transcription	GM12878-XiMat	blood
38	chr12:48516400-48545400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:48516400-48545800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:48516400-48547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:48516400-48547200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr12:48516400-48547800	Strong transcription	Fetal Stomach	stomach
43	chr12:48516600-48525000	Weak transcription	Fetal Intestine Small	intestine
44	chr12:48516600-48525000	Weak transcription	Right Atrium	heart
45	chr12:48516600-48527800	Weak transcription	Small Intestine	intestine
46	chr12:48516600-48536600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:48516600-48543200	Weak transcription	Stomach Mucosa	stomach
48	chr12:48516600-48545400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:48516600-48545600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:48516800-48529400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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