Variant report

Variant	rs11656408
Chromosome Location	chr17:28637173-28637174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1050565	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11867581	0.80[EUR][1000 genomes]
rs12938714	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12939390	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12941223	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12945042	0.86[ASN][1000 genomes]
rs12949747	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13341611	0.81[EUR][1000 genomes]
rs17767256	0.83[ASN][1000 genomes]
rs2321706	0.89[ASN][1000 genomes]
rs3103303	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3103306	0.89[ASN][1000 genomes]
rs3110060	0.85[ASN][1000 genomes]
rs3110061	0.85[ASN][1000 genomes]
rs3110452	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3110454	0.85[ASN][1000 genomes]
rs33980254	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34353378	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34622227	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35724800	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs36000555	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36048853	0.94[ASN][1000 genomes]
rs3764449	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3794806	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6505171	0.80[EUR][1000 genomes]
rs6505173	0.82[EUR][1000 genomes]
rs7208052	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7214248	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7223821	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73268099	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7342921	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8073378	0.80[EUR][1000 genomes]
rs8078900	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8080149	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8080300	0.80[EUR][1000 genomes]
rs998087	0.85[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	nsv1064975	chr17:28604187-28851905	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv543299	chr17:28604187-28851905	Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv543300	chr17:28620420-28659310	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11656408	BLMH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:28636200-28639000	Weak transcription	Fetal Intestine Small	intestine
2	chr17:28636200-28639400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr17:28636600-28639000	Weak transcription	Fetal Intestine Large	intestine
4	chr17:28636800-28637200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:28636800-28640000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr17:28637000-28638000	Weak transcription	NH-A	brain
7	chr17:28637000-28639000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:28637000-28639400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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