Variant report

Variant	rs342520
Chromosome Location	chr3:42534042-42534043
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	chr3:42533518..42535270-chr3:42539632..42541675,2	MCF-7	breast:
2	chr3:42529090..42533443-chr3:42533713..42536852,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11129965	1.00[JPT][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs342520	CCR9	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42528200-42535400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:42530200-42535200	Enhancers	Placenta	Placenta
3	chr3:42530200-42535600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:42530200-42535600	Enhancers	Lung	lung
5	chr3:42530800-42535000	Enhancers	Primary B cells from cord blood	blood
6	chr3:42530800-42535000	Enhancers	Primary B cells from peripheral blood	blood
7	chr3:42531000-42534400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:42532200-42534200	Weak transcription	Right Atrium	heart
9	chr3:42532200-42534400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:42532200-42534800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:42532200-42538800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:42532400-42534600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:42532400-42535600	Enhancers	GM12878-XiMat	blood
14	chr3:42532600-42535400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:42532600-42537600	Weak transcription	Hela-S3	cervix
16	chr3:42532600-42537800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:42532600-42538000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:42532600-42538000	Weak transcription	A549	lung
19	chr3:42532600-42538400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:42532600-42538400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:42532600-42538600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:42532600-42538800	Weak transcription	Esophagus	oesophagus
23	chr3:42532800-42534200	Weak transcription	Fetal Heart	heart
24	chr3:42532800-42537800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:42533200-42534400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr3:42533200-42534600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:42533200-42534600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr3:42533400-42535000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:42533600-42534200	Enhancers	Liver	Liver
30	chr3:42533600-42534200	Enhancers	Stomach Mucosa	stomach
31	chr3:42533600-42534200	Enhancers	HUVEC	blood vessel
32	chr3:42533600-42534400	Enhancers	Fetal Lung	lung
33	chr3:42533600-42534600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:42533600-42534600	Enhancers	Spleen	Spleen
35	chr3:42533600-42535600	Enhancers	Adipose Nuclei	Adipose
36	chr3:42533800-42534200	Enhancers	Gastric	stomach
37	chr3:42533800-42534400	Enhancers	Fetal Muscle Leg	muscle
38	chr3:42533800-42534800	Enhancers	Right Ventricle	heart
39	chr3:42533800-42535000	Enhancers	Duodenum Mucosa	Duodenum
40	chr3:42533800-42535000	Enhancers	Left Ventricle	heart
41	chr3:42533800-42538600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:42534000-42535200	Enhancers	Pancreas	Pancrea
43	chr3:42534000-42538600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:42534000-42539600	Weak transcription	Brain Cingulate Gyrus	brain

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