Variant report

Variant	rs11217987
Chromosome Location	chr11:120579826-120579827
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	chr11:120572331..120575238-chr11:120578976..120580756,3	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11217978	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11217979	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11217980	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11217981	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11217983	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11217984	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11217988	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11217989	1.00[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11603713	0.82[CHB][hapmap]
rs11604327	0.82[CHB][hapmap]
rs12270261	0.81[CEU][hapmap]
rs12270409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12272864	0.81[CEU][hapmap]
rs12274300	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12276408	0.86[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12276440	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12278795	0.81[CEU][hapmap]
rs12280296	0.81[CEU][hapmap]
rs12281464	0.91[CEU][hapmap];0.82[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12281614	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12291927	0.81[CEU][hapmap]
rs12293393	0.81[CEU][hapmap]
rs12294858	0.85[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12295113	0.81[CEU][hapmap]
rs12295200	0.81[CEU][hapmap]
rs17124211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17124222	0.82[CHB][hapmap]
rs2846109	0.81[CEU][hapmap]
rs2852225	0.81[CEU][hapmap]
rs2852227	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs28781001	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4451741	0.82[CHB][hapmap]
rs4567478	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61901379	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61901380	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61902685	0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61902688	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7102869	0.81[CEU][hapmap]
rs7103021	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7103228	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs7103418	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7119619	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7944756	0.91[CEU][hapmap]
rs7946325	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630199	0.90[CEU][hapmap];0.82[CHB][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9630200	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9630201	0.82[CHB][hapmap]

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	nsv1054407	chr11:120535570-120630114	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1053607	chr11:120540795-120802006	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3693392	chr11:120549745-120628012	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11217987	FXYD6	cis	parietal	SCAN
rs11217987	TAGLN	cis	parietal	SCAN
rs11217987	C2CD2L	cis	parietal	SCAN
rs11217987	POU2F3	cis	parietal	SCAN
rs11217987	TMEM136	cis	cerebellum	SCAN
rs11217987	MCAM	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120568000-120580600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr11:120570000-120581600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:120578200-120580600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:120578600-120581600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:120578800-120580400	Weak transcription	Fetal Lung	lung
6	chr11:120578800-120580800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:120578800-120581000	Weak transcription	Ovary	ovary
8	chr11:120579000-120580600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:120579000-120581200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr11:120579000-120583000	Enhancers	Fetal Intestine Large	intestine
11	chr11:120579200-120580200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:120579200-120580200	Enhancers	Fetal Intestine Small	intestine
13	chr11:120579200-120580400	Enhancers	GM12878-XiMat	blood
14	chr11:120579200-120585200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:120579400-120580400	Weak transcription	Adipose Nuclei	Adipose
16	chr11:120579400-120580800	Enhancers	HepG2	liver
17	chr11:120579600-120581000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:120579800-120581200	Weak transcription	Left Ventricle	heart
19	chr11:120579800-120581400	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links