Variant report

Variant	rs11129965
Chromosome Location	chr3:42518379-42518380
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42513067..42515977-chr3:42516724..42519478,3	MCF-7	breast:
2	chr3:42518243..42520481-chr3:42527849..42529639,2	K562	blood:
3	chr3:42514438..42520179-chr3:42543715..42548032,5	MCF-7	breast:
4	chr3:42514055..42518453-chr3:42530797..42534377,7	MCF-7	breast:
5	chr3:42517728..42519820-chr3:42622066..42624562,2	MCF-7	breast:
6	chr3:42518174..42522786-chr3:42527620..42534309,10	MCF-7	breast:
7	chr3:42518210..42518927-chr7:1628754..1629545,2	MCF-7	breast:
8	chr3:42515854..42518647-chr3:42520665..42522893,2	MCF-7	breast:
9	chr3:42517238..42518922-chr3:42524416..42526757,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000114812	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17074496	0.82[CHB][hapmap]
rs191767	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs342520	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs342527	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342529	0.82[CEU][hapmap]
rs543673	0.82[CEU][hapmap]
rs7635496	0.82[CHB][hapmap]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11129965	CCR9	cis	parietal	SCAN
rs11129965	TMEM42	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42513400-42519600	Enhancers	Spleen	Spleen
2	chr3:42514400-42519200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:42515200-42518400	Weak transcription	Pancreas	Pancrea
4	chr3:42516800-42518800	Enhancers	Esophagus	oesophagus
5	chr3:42517400-42519200	Enhancers	HMEC	breast
6	chr3:42517400-42519600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:42517400-42520600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:42517600-42518600	Enhancers	HUVEC	blood vessel
9	chr3:42517600-42519000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr3:42517600-42519200	Enhancers	Placenta	Placenta
11	chr3:42517600-42519200	Enhancers	NHEK	skin
12	chr3:42517600-42519400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:42517800-42518600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:42517800-42518800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:42517800-42519000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:42517800-42519000	Enhancers	Gastric	stomach
17	chr3:42517800-42519000	Enhancers	Hela-S3	cervix
18	chr3:42517800-42519200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:42517800-42519200	Enhancers	Stomach Mucosa	stomach
20	chr3:42517800-42519400	Enhancers	Lung	lung
21	chr3:42518000-42518400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:42518000-42518600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr3:42518000-42518800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr3:42518000-42519000	Enhancers	Adipose Nuclei	Adipose
25	chr3:42518000-42519000	Enhancers	HSMMtube	muscle
26	chr3:42518000-42519200	Enhancers	Duodenum Mucosa	Duodenum
27	chr3:42518000-42519400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:42518200-42518600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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