Variant report

Variant	rs11249969
Chromosome Location	chr8:9931978-9931979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9930550..9933030-chr8:9938731..9941412,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10107485	0.85[CHB][hapmap]
rs11249968	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11249970	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1160369	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[MEX][hapmap]
rs11774411	0.86[CHB][hapmap]
rs11779614	0.82[ASN][1000 genomes]
rs11783851	0.86[CHB][hapmap]
rs11785434	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs12155541	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12542030	0.91[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12545775	0.81[JPT][hapmap]
rs12545788	0.81[JPT][hapmap]
rs12545826	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs12547884	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12549943	0.82[CHB][hapmap]
rs12550244	0.83[CHB][hapmap]
rs12550614	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12679328	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12680389	0.86[JPT][hapmap]
rs13249013	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs13250499	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13256357	0.81[CHB][hapmap]
rs13261836	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13279619	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1484641	0.81[YRI][hapmap]
rs1484645	0.82[CHB][hapmap]
rs1521193	0.82[EUR][1000 genomes]
rs1564808	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs17151190	0.82[CHB][hapmap]
rs17155393	0.81[JPT][hapmap]
rs2409632	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2628138	0.91[EUR][1000 genomes]
rs2898242	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs35349653	0.84[ASN][1000 genomes]
rs3735823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4294187	0.83[CHB][hapmap]
rs4840462	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4840463	0.87[CEU][hapmap]
rs4841277	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4841279	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs625218	0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs685218	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6981546	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6983566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6992096	0.82[EUR][1000 genomes]
rs6992152	0.82[EUR][1000 genomes]
rs6997865	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7008407	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs7012221	0.86[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7831989	0.89[EUR][1000 genomes]
rs7832431	0.91[CEU][hapmap];0.83[CHB][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes]
rs9329215	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs9644681	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv869934	chr8:9806639-9940586	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv890343	chr8:9888729-9932797	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1018236	chr8:9915428-9940481	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11249969	MSRA	cis	lymphoblastoid	seeQTL
rs11249969	LONRF1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9913000-9933400	Weak transcription	Gastric	stomach
2	chr8:9913200-9933600	Weak transcription	Pancreas	Pancrea
3	chr8:9913200-9944800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:9913400-9935800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:9913600-9938600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr8:9914800-9947200	Weak transcription	Left Ventricle	heart
7	chr8:9920200-9938400	Weak transcription	Spleen	Spleen
8	chr8:9926400-9940400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr8:9928400-9933800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr8:9929600-9947200	Weak transcription	Aorta	Aorta
11	chr8:9930200-9934200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr8:9930200-9937200	Weak transcription	Primary B cells from cord blood	blood
13	chr8:9931200-9939600	Weak transcription	Primary T cells from cord blood	blood
14	chr8:9931200-9940200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr8:9931400-9933400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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