Variant report

Variant	rs12655898
Chromosome Location	chr5:17259511-17259512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:17255104..17256658-chr5:17257028..17259986,2	MCF-7	breast:
2	chr5:17258796..17260923-chr5:17271859..17273563,2	MCF-7	breast:
3	chr5:17216171..17217892-chr5:17257911..17259730,2	MCF-7	breast:
4	chr5:17218090..17220467-chr5:17258219..17260640,2	MCF-7	breast:
5	chr5:17251354..17254126-chr5:17258687..17261366,3	MCF-7	breast:
6	chr5:17238715..17240900-chr5:17259228..17262117,2	K562	blood:

Variant related genes	Relation type
ENSG00000215196	Chromatin interaction
ENSG00000176788	Chromatin interaction
ENSG00000252908	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3733748	1.00[EUR][1000 genomes]
rs6899153	1.00[EUR][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	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv830218	chr5:17093162-17290045	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17229800-17261600	Weak transcription	Fetal Stomach	stomach
2	chr5:17232800-17260000	Weak transcription	Fetal Kidney	kidney
3	chr5:17232800-17278800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:17242800-17275000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:17244800-17274600	Weak transcription	Ovary	ovary
6	chr5:17249400-17275200	Weak transcription	Aorta	Aorta
7	chr5:17252800-17260800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:17252800-17271200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:17254200-17259600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:17255600-17260800	Enhancers	Fetal Brain Male	brain
11	chr5:17256000-17261400	Weak transcription	Fetal Lung	lung
12	chr5:17256200-17279800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:17256400-17260200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr5:17256400-17274600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:17256600-17275200	Weak transcription	Placenta	Placenta
16	chr5:17257600-17259800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr5:17257600-17259800	ZNF genes & repeats	A549	lung
18	chr5:17257600-17260600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:17257600-17260800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:17257800-17261600	ZNF genes & repeats	GM12878-XiMat	blood
21	chr5:17258000-17260200	Weak transcription	Brain Angular Gyrus	brain
22	chr5:17258200-17259600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:17258200-17260000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:17258200-17274600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:17258400-17259800	Weak transcription	Fetal Brain Female	brain
26	chr5:17258400-17260200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:17258400-17262200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:17258800-17259800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:17258800-17260400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:17258800-17261000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr5:17259000-17259800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:17259000-17259800	Weak transcription	Brain Germinal Matrix	brain
33	chr5:17259000-17259800	Weak transcription	NHLF	lung
34	chr5:17259000-17261200	Weak transcription	NHEK	skin
35	chr5:17259000-17263600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:17259000-17263600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:17259000-17274600	Weak transcription	HSMMtube	muscle
38	chr5:17259000-17274800	Weak transcription	Osteobl	bone
39	chr5:17259000-17275800	Weak transcription	HMEC	breast
40	chr5:17259000-17276000	Weak transcription	HSMM	muscle
41	chr5:17259200-17259600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:17259200-17259600	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr5:17259200-17259600	Weak transcription	NHDF-Ad	bronchial
44	chr5:17259200-17259800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:17259200-17259800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:17259200-17259800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr5:17259200-17259800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:17259200-17259800	Weak transcription	Primary B cells from cord blood	blood
49	chr5:17259200-17259800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:17259200-17260000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links