Variant report

Variant	rs56164300
Chromosome Location	chr11:65557904-65557905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:65557860-65558010	A549	lung:	n/a	chr11:65557861-65557870

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65478230..65480937-chr11:65556981..65559484,3	MCF-7	breast:
2	chr11:65546714..65547677-chr11:65557876..65558611,3	MCF-7	breast:
3	chr11:65544951..65562337-chr11:65623093..65630859,34	MCF-7	breast:
4	chr11:65556129..65558020-chr11:65687401..65689807,2	MCF-7	breast:
5	chr11:65547507..65549362-chr11:65557835..65559340,2	K562	blood:
6	chr11:65556556..65561389-chr11:65623769..65628916,7	MCF-7	breast:
7	chr11:65416969..65422455-chr11:65556396..65561611,5	MCF-7	breast:
8	chr11:65557488..65562536-chr11:65655379..65657877,5	K562	blood:
9	chr11:65556531..65558931-chr11:65624353..65626096,2	K562	blood:
10	chr11:65557488..65560218-chr11:65655379..65657652,3	K562	blood:
11	chr11:65479410..65482518-chr11:65556440..65559162,4	MCF-7	breast:
12	chr11:65477923..65479953-chr11:65556662..65559648,2	K562	blood:
13	chr11:65546169..65552016-chr11:65555022..65558350,9	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX32-2	chr11:65557600-65557959	NONHSAT022214

No data

Variant related genes	Relation type
OVOL1	TF binding region
OVOL1-AS1	TF binding region
ENSG00000172757	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000213445	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000254470	Chromatin interaction
ENSG00000175827	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11600035	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11603206	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12802560	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2277304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34509162	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36008241	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs491666	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs501337	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs523521	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs530405	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs553980	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs554863	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs561924	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs601683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs604949	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67901563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67995174	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71197355	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv897760	chr11:65545306-65559266	Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65555800-65558200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:65555800-65558800	Weak transcription	Right Atrium	heart
3	chr11:65555800-65562000	Enhancers	HMEC	breast
4	chr11:65556000-65558200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:65556000-65558600	Enhancers	Gastric	stomach
6	chr11:65556000-65558800	Weak transcription	Lung	lung
7	chr11:65556000-65559400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:65556000-65562000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr11:65556200-65558200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr11:65556200-65558200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
11	chr11:65556200-65561600	Enhancers	Pancreas	Pancrea
12	chr11:65556400-65558000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr11:65556400-65561600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:65556400-65561800	Enhancers	Stomach Mucosa	stomach
15	chr11:65556600-65558200	Bivalent Enhancer	Placenta	Placenta
16	chr11:65556600-65558400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr11:65557200-65558000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:65557200-65558200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr11:65557200-65558400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr11:65557400-65558000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:65557400-65558000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr11:65557400-65558400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr11:65557400-65558400	Weak transcription	GM12878-XiMat	blood
24	chr11:65557400-65563800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:65557600-65558400	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr11:65557600-65558400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr11:65557600-65559200	Flanking Active TSS	Colonic Mucosa	Colon
28	chr11:65557800-65558000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:65557800-65558000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:65557800-65558000	Flanking Active TSS	Fetal Intestine Large	intestine
31	chr11:65557800-65558200	Transcr. at gene 5' and 3'	Esophagus	oesophagus
32	chr11:65557800-65558200	Enhancers	Fetal Kidney	kidney
33	chr11:65557800-65558400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
34	chr11:65557800-65558400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
35	chr11:65557800-65559800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr11:65557800-65559800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr11:65557800-65560000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr11:65557800-65561200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr11:65557800-65561600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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