Variant report

Variant	rs656007
Chromosome Location	chr11:75377226-75377227
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75271851..75274774-chr11:75376979..75378673,2	K562	blood:
2	chr11:75371977..75373733-chr11:75376017..75378232,2	K562	blood:
3	chr11:75369616..75372196-chr11:75374658..75377795,3	MCF-7	breast:
4	chr11:75369962..75371623-chr11:75376445..75378438,2	K562	blood:
5	chr11:75362323..75365214-chr11:75375705..75377919,2	K562	blood:

Variant related genes	Relation type
ENSG00000149257	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1145696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1234668	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2508193	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944086	0.87[TSI][hapmap]
rs512500	0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs541993	0.91[CEU][hapmap];0.80[GIH][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes]
rs544698	0.91[EUR][1000 genomes]
rs546156	0.91[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs590550	0.87[TSI][hapmap]
rs604694	0.85[ASW][hapmap];0.81[CEU][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs640927	0.90[MEX][hapmap]
rs641976	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs652452	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs654949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs657639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs660343	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs663515	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs668378	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs687793	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7110142	0.87[TSI][hapmap]
rs7114999	0.87[TSI][hapmap]
rs7128846	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7947980	0.87[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs656007	SLCO2B1	cis	lymphoblastoid	seeQTL
rs656007	ITGB2	trans	lymphoblastoid	seeQTL
rs656007	RAB6A	cis	cerebellum	SCAN
rs656007	RELT	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75364600-75378000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr11:75367400-75377800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:75367600-75378200	Weak transcription	Aorta	Aorta
4	chr11:75367800-75377800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:75373600-75377400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:75375400-75377600	Flanking Active TSS	Fetal Brain Female	brain
7	chr11:75375400-75378000	Weak transcription	Pancreas	Pancrea
8	chr11:75375600-75378000	Weak transcription	Spleen	Spleen
9	chr11:75376000-75377400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:75376400-75378000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:75376400-75378000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr11:75376600-75377400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:75376600-75377800	Active TSS	Brain Angular Gyrus	brain
14	chr11:75376600-75377800	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr11:75376600-75378000	Active TSS	Brain Cingulate Gyrus	brain
16	chr11:75376600-75380200	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr11:75376600-75380600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:75377000-75377800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:75377000-75378400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr11:75377200-75377600	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr11:75377200-75377600	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr11:75377200-75378400	Active TSS	Fetal Brain Male	brain
23	chr11:75377200-75378600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links