Variant report

Variant	rs11130540
Chromosome Location	chr3:56726105-56726106
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56715854..56718511-chr3:56721135..56727135,8	MCF-7	breast:
2	chr3:56715900..56719627-chr3:56722769..56727051,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10049468	0.90[EUR][1000 genomes]
rs11130537	0.90[EUR][1000 genomes]
rs11130541	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1565373	0.81[EUR][1000 genomes]
rs1565375	0.82[EUR][1000 genomes]
rs2317244	0.84[EUR][1000 genomes]
rs2317252	0.90[EUR][1000 genomes]
rs4234393	0.89[EUR][1000 genomes]
rs4681734	0.89[EUR][1000 genomes]
rs4681740	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4681933	0.84[EUR][1000 genomes]
rs4681945	0.87[EUR][1000 genomes]
rs4681964	0.85[EUR][1000 genomes]
rs4681980	0.91[EUR][1000 genomes]
rs4681994	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4682000	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62251242	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6445803	0.85[EUR][1000 genomes]
rs6445804	0.83[EUR][1000 genomes]
rs6445810	0.90[EUR][1000 genomes]
rs6445814	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6787227	0.91[EUR][1000 genomes]
rs6802498	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6809499	0.90[EUR][1000 genomes]
rs7618007	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7619465	0.91[EUR][1000 genomes]
rs7620259	0.84[EUR][1000 genomes]
rs7631662	0.91[EUR][1000 genomes]
rs7642389	0.89[EUR][1000 genomes]
rs9311614	0.82[EUR][1000 genomes]
rs9809309	0.89[EUR][1000 genomes]
rs9835332	0.85[EUR][1000 genomes]
rs9839065	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9851653	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9858568	0.83[EUR][1000 genomes]
rs9875257	0.89[EUR][1000 genomes]
rs9878373	0.85[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11130540	CCDC66	cis	Thyroid	GTEx
rs11130540	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56717800-56726800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:56718000-56727000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:56718000-56727400	Weak transcription	HSMMtube	muscle
4	chr3:56718400-56727000	Weak transcription	HSMM	muscle
5	chr3:56718800-56726600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:56722400-56726600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:56722400-56727000	Weak transcription	Primary B cells from cord blood	blood
8	chr3:56722600-56726800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:56723600-56727000	Weak transcription	GM12878-XiMat	blood
10	chr3:56725200-56726200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:56725200-56726200	Enhancers	HMEC	breast
12	chr3:56725200-56726800	Enhancers	Dnd41	blood
13	chr3:56725600-56726800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:56725800-56734000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:56726000-56726400	Weak transcription	Fetal Thymus	thymus
16	chr3:56726000-56727800	Weak transcription	Placenta	Placenta
17	chr3:56726000-56734000	Weak transcription	NHEK	skin

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