Variant report

Variant	rs2516715
Chromosome Location	chr6:30226165-30226166
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:30226110-30228388	H1-hESC	embryonic stem cell:	n/a	chr6:30227308-30227317
2	POLR2A	chr6:30225935-30226299	GM12892	blood:	n/a	n/a
3	RFX5	chr6:30225760-30229308	IMR90	lung:	n/a	chr6:30226089-30226097 chr6:30227308-30227317
4	TAF1	chr6:30225980-30226185	GM12892	blood:	n/a	n/a
5	YY1	chr6:30225985-30226253	GM12892	blood:	n/a	n/a
6	BATF	chr6:30225980-30226197	GM12878	blood:	n/a	n/a
7	RFX5	chr6:30225288-30228368	SK-N-SH	brain:	n/a	chr6:30226089-30226097 chr6:30227308-30227317
8	BATF	chr6:30225922-30226232	GM12878	blood:	n/a	n/a
9	SPI1	chr6:30225923-30226204	GM12891	blood:	n/a	n/a
10	POLR2A	chr6:30225922-30226351	GM12892	blood:	n/a	n/a
11	POLR2A	chr6:30225929-30226271	GM12892	blood:	n/a	n/a
12	EBF1	chr6:30226013-30226222	GM12878	blood:	n/a	n/a
13	SPI1	chr6:30225912-30226221	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30226094..30227681-chr6:30293299..30296159,2	MCF-7	breast:
2	chr6:30225449..30228967-chr6:30292795..30296377,4	K562	blood:
3	chr6:30224455..30226644-chr6:30292386..30294096,2	MCF-7	breast:
4	chr6:30225542..30228363-chr6:30311426..30313496,2	MCF-7	breast:

Variant related genes	Relation type
HLA-L	TF binding region
ENSG00000231074	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000204599	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1075105	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12055553	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12192505	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1264617	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1264618	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1264619	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2187979	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2428506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2516696	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523740	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs261947	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2844759	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2844760	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2844762	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844766	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711213	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6900042	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6906180	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6912771	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6913293	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6924282	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6924453	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6931387	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9295842	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9357098	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9368635	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9380167	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9380172	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2516715	TRIM26	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30225200-30226600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:30225200-30226800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:30225800-30227000	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr6:30226000-30226200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:30226000-30226200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr6:30226000-30226200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:30226000-30226200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:30226000-30226200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
9	chr6:30226000-30226200	Enhancers	Esophagus	oesophagus
10	chr6:30226000-30226200	Enhancers	Spleen	Spleen
11	chr6:30226000-30226200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
12	chr6:30226000-30226400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr6:30226000-30226800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr6:30226000-30226800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr6:30226000-30226800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:30226000-30226800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:30226000-30226800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
18	chr6:30226000-30226800	Enhancers	Primary B cells from peripheral blood	blood
19	chr6:30226000-30226800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr6:30226000-30226800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr6:30226000-30226800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:30226000-30226800	Enhancers	GM12878-XiMat	blood
23	chr6:30226000-30226800	Bivalent Enhancer	HepG2	liver
24	chr6:30226000-30227000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr6:30226000-30227000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:30226000-30227000	Enhancers	Pancreas	Pancrea
27	chr6:30226000-30227200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:30226000-30227200	Enhancers	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links