Variant report

Variant	rs491666
Chromosome Location	chr11:65564035-65564036
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65551696..65553777-chr11:65562013..65564216,2	K562	blood:
2	chr11:65429991..65432005-chr11:65562169..65564755,2	K562	blood:
3	chr11:65562689..65566411-chr11:65620359..65624603,6	K562	blood:
4	chr11:65546923..65549109-chr11:65560977..65565317,4	K562	blood:
5	chr11:65563461..65568166-chr11:65728932..65730847,4	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-770G2.3.1-2	chr11:65563417-65564100	ENSG00000255404.1

No data

Variant related genes	Relation type
ENSG00000175827	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000254470	Chromatin interaction
ENSG00000172757	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11227266	1.00[CHB][hapmap]
rs11600035	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11603206	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12802560	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17491607	1.00[JPT][hapmap]
rs2277304	0.87[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34509162	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36008241	0.87[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs501337	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523521	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553980	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554863	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56164300	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs561924	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs601683	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs604949	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67901563	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67995174	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71197355	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732072	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
4	nsv897758	chr11:65490756-65564035	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
7	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs491666	TAF6L	cis	cerebellum	SCAN
rs491666	PRDX5	cis	parietal	SCAN
rs491666	TCIRG1	cis	parietal	SCAN
rs491666	KAT5	cis	cerebellum	SCAN
rs491666	KCNK4	cis	cerebellum	SCAN
rs491666	PKM2	trans	parietal	SCAN
rs491666	RNASEH2C	cis	parietal	SCAN
rs491666	SNX32	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65558000-65564400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:65558200-65564800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:65558200-65568800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr11:65558400-65566200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr11:65559200-65566000	Weak transcription	Small Intestine	intestine
6	chr11:65559800-65570600	Weak transcription	Spleen	Spleen
7	chr11:65560400-65565600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:65560800-65564600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:65561800-65564200	Weak transcription	Stomach Mucosa	stomach
10	chr11:65561800-65564400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr11:65562000-65564200	Strong transcription	Colonic Mucosa	Colon
12	chr11:65562000-65564400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:65562000-65565600	Weak transcription	HMEC	breast
14	chr11:65562200-65564400	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr11:65562200-65566200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:65562600-65564200	Strong transcription	Fetal Intestine Small	intestine
17	chr11:65562600-65564800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr11:65562600-65564800	Strong transcription	Esophagus	oesophagus
19	chr11:65562600-65565400	Strong transcription	Fetal Intestine Large	intestine
20	chr11:65562800-65564200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:65562800-65568600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:65563000-65566200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:65563200-65565000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:65563400-65566400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:65563400-65567600	Weak transcription	Gastric	stomach
26	chr11:65563400-65576200	Weak transcription	Pancreas	Pancrea
27	chr11:65563600-65564200	Genic enhancers	Placenta	Placenta
28	chr11:65563800-65566200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr11:65563800-65566800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:65563800-65566800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:65563800-65571000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr11:65564000-65565200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr11:65564000-65566000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:65564000-65566600	Weak transcription	H9 Cell Line	embryonic stem cell

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