Variant report

Variant	rs11988798
Chromosome Location	chr8:61330014-61330015
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61325999..61328203-chr8:61328768..61330939,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251396	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10087760	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10092773	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10102945	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10504312	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11988766	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12548711	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1318227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1552070	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1842388	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1893277	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1893279	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1941467	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2012856	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2068587	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2155831	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6471873	0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6471877	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6471880	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6471881	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6982032	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6982404	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6986664	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6994192	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6998307	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6999822	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7001436	0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7004236	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7005668	0.83[ASN][1000 genomes]
rs7814226	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7819947	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7824474	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7824671	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7828383	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7831106	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7841648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9785091	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS 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	74 gene(s)	inside rSNPs	diseases
2	esv3371465	chr8:61115030-61356658	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv831334	chr8:61148796-61330190	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11988798	RP11-163N6.2	cis	Thyroid	GTEx
rs11988798	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61325600-61330200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr8:61329400-61330800	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr8:61329600-61330200	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links