Variant report

Variant	rs11130082
Chromosome Location	chr3:46025518-46025519
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	chr3:46024602..46026106-chr3:46028613..46030507,2	MCF-7	breast:
2	chr3:46015505..46018391-chr3:46024106..46026296,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12053895	0.81[EUR][1000 genomes]
rs12485445	0.81[EUR][1000 genomes]
rs13064616	0.81[EUR][1000 genomes]
rs13084541	0.81[EUR][1000 genomes]
rs13086858	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1392298	0.80[EUR][1000 genomes]
rs1500003	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1545985	0.91[CEU][hapmap]
rs1846615	0.94[EUR][1000 genomes]
rs1846616	0.84[EUR][1000 genomes]
rs1873000	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1873001	0.88[CEU][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2129879	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2129881	0.81[EUR][1000 genomes]
rs2133660	0.92[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2171528	0.88[CEU][hapmap]
rs2171529	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2373089	0.81[EUR][1000 genomes]
rs2373090	0.81[EUR][1000 genomes]
rs35283688	0.81[EUR][1000 genomes]
rs4683159	1.00[CEU][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57542549	0.81[EUR][1000 genomes]
rs6774629	0.80[EUR][1000 genomes]
rs7612402	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7628447	1.00[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869609	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking 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	29 gene(s)	inside rSNPs	diseases
3	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11130082	CCR3	cis	Whole Blood	GTEx
rs11130082	FYCO1	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45986400-46026600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:45987200-46027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:45987400-46026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:45987800-46026400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:45987800-46026800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:45987800-46027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:45988000-46026600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:46000000-46029600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:46002600-46027200	Weak transcription	A549	lung
11	chr3:46008600-46026400	Strong transcription	Hela-S3	cervix
12	chr3:46009000-46027800	Weak transcription	Fetal Brain Male	brain
13	chr3:46010200-46027000	Weak transcription	Fetal Brain Female	brain
14	chr3:46010200-46029600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:46010200-46033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:46013000-46026200	Weak transcription	Brain Germinal Matrix	brain
17	chr3:46013600-46025600	Strong transcription	Fetal Stomach	stomach
18	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
19	chr3:46014000-46025800	Strong transcription	HepG2	liver
20	chr3:46014000-46026400	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr3:46014200-46026000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:46015400-46026400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:46015600-46027200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:46015800-46026400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:46015800-46026800	Strong transcription	Brain Hippocampus Middle	brain
26	chr3:46015800-46027600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:46016000-46026600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:46016200-46027800	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr3:46017600-46026200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:46018000-46025800	Strong transcription	Lung	lung
31	chr3:46018800-46026800	Strong transcription	Primary hematopoietic stem cells	blood
32	chr3:46019200-46026800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:46019400-46030000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:46019600-46026200	Strong transcription	Adipose Nuclei	Adipose
35	chr3:46020000-46034200	Genic enhancers	Dnd41	blood
36	chr3:46020400-46027200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:46020800-46027000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:46021000-46025600	Strong transcription	Fetal Lung	lung
39	chr3:46021400-46026800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:46021400-46028200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:46021400-46036200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:46021600-46025800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr3:46021600-46026400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr3:46021600-46034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:46021800-46026600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:46022200-46026000	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr3:46022200-46026200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:46022400-46025800	Strong transcription	Brain Substantia Nigra	brain
49	chr3:46022400-46026400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:46022400-46027400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links