Variant report

Variant	rs10490605
Chromosome Location	chr2:172118473-172118474
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	chr2:172118370..172120069-chr2:172136015..172138114,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10754977	0.92[ASN][1000 genomes]
rs10803858	0.92[ASN][1000 genomes]
rs10803859	0.87[ASN][1000 genomes]
rs10930464	0.92[ASN][1000 genomes]
rs11903215	0.87[ASN][1000 genomes]
rs12474103	0.94[ASN][1000 genomes]
rs13007471	0.90[CEU][hapmap];0.94[ASN][1000 genomes]
rs34931272	0.94[ASN][1000 genomes]
rs4584997	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs6727785	0.87[ASN][1000 genomes]
rs6743965	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10490605	SELV	trans	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172102800-172127400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:172103200-172120000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:172112000-172118600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:172116400-172118800	Enhancers	Dnd41	blood
5	chr2:172116800-172118600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:172116800-172118600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:172116800-172119000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr2:172116800-172119000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr2:172116800-172119000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr2:172116800-172119600	Enhancers	Primary hematopoietic stem cells	blood
11	chr2:172116800-172120000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:172117200-172118800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:172117200-172119000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:172117400-172119600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:172117400-172120400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr2:172117600-172118600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:172117600-172118600	Weak transcription	NHEK	skin
18	chr2:172117600-172118800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:172117600-172119000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:172117600-172119000	Enhancers	GM12878-XiMat	blood
21	chr2:172117600-172119200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr2:172117600-172122400	Weak transcription	Primary B cells from cord blood	blood
23	chr2:172117600-172122600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:172117800-172118800	Weak transcription	HepG2	liver
25	chr2:172117800-172120200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:172118000-172119000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:172118000-172119200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:172118200-172118600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:172118200-172119000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:172118200-172119000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr2:172118200-172119000	Enhancers	Brain Substantia Nigra	brain
32	chr2:172118200-172119200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:172118200-172119200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr2:172118400-172118600	Enhancers	Colon Smooth Muscle	Colon
35	chr2:172118400-172118800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:172118400-172118800	Enhancers	Brain Hippocampus Middle	brain
37	chr2:172118400-172119000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr2:172118400-172119000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:172118400-172122400	Weak transcription	Primary B cells from peripheral blood	blood

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