Variant report

Variant	rs2277304
Chromosome Location	chr11:65558309-65558310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:65558160-65558310	NHEK	skin:	n/a	n/a
2	CTCF	chr11:65558160-65558310	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:12 , 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	chr11:65547507..65549362-chr11:65557835..65559340,2	K562	blood:
5	chr11:65556556..65561389-chr11:65623769..65628916,7	MCF-7	breast:
6	chr11:65416969..65422455-chr11:65556396..65561611,5	MCF-7	breast:
7	chr11:65557488..65562536-chr11:65655379..65657877,5	K562	blood:
8	chr11:65556531..65558931-chr11:65624353..65626096,2	K562	blood:
9	chr11:65557488..65560218-chr11:65655379..65657652,3	K562	blood:
10	chr11:65479410..65482518-chr11:65556440..65559162,4	MCF-7	breast:
11	chr11:65477923..65479953-chr11:65556662..65559648,2	K562	blood:
12	chr11:65546169..65552016-chr11:65555022..65558350,9	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-770G2.3.1-1	chr11:65558233-65558339	ENSG00000255120.1
2	lnc-RP11-770G2.3.1-1	chr11:65558233-65558555	NONHSAT022212
3	lnc-RP11-770G2.3.1-1	chr11:65558233-65558339	NR_108085

No data

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

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11600035	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603206	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12802560	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17491607	1.00[JPT][hapmap]
rs34509162	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36008241	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491666	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]
rs501337	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs523521	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][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];0.86[ASN][1000 genomes]
rs554863	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56164300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs561924	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604949	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67901563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67995174	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71197355	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs732072	1.00[JPT][hapmap]

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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2277304	RNASEH2C	cis	parietal	SCAN
rs2277304	KAT5	cis	cerebellum	SCAN
rs2277304	PKM2	trans	parietal	SCAN
rs2277304	PRDX5	cis	parietal	SCAN
rs2277304	TCIRG1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65555800-65558800	Weak transcription	Right Atrium	heart
2	chr11:65555800-65562000	Enhancers	HMEC	breast
3	chr11:65556000-65558600	Enhancers	Gastric	stomach
4	chr11:65556000-65558800	Weak transcription	Lung	lung
5	chr11:65556000-65559400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:65556000-65562000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr11:65556200-65561600	Enhancers	Pancreas	Pancrea
8	chr11:65556400-65561600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:65556400-65561800	Enhancers	Stomach Mucosa	stomach
10	chr11:65556600-65558400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr11:65557200-65558400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr11:65557400-65558400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr11:65557400-65558400	Weak transcription	GM12878-XiMat	blood
14	chr11:65557400-65563800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:65557600-65558400	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr11:65557600-65558400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:65557600-65559200	Flanking Active TSS	Colonic Mucosa	Colon
18	chr11:65557800-65558400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
19	chr11:65557800-65558400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
20	chr11:65557800-65559800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:65557800-65559800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr11:65557800-65560000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr11:65557800-65561200	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr11:65557800-65561600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:65558000-65558600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:65558000-65558600	Enhancers	Fetal Intestine Large	intestine
27	chr11:65558000-65558800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:65558000-65559200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:65558000-65560600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr11:65558000-65562000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:65558000-65564400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:65558200-65558400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:65558200-65558600	Active TSS	Esophagus	oesophagus
34	chr11:65558200-65560200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr11:65558200-65560600	Enhancers	Placenta	Placenta
36	chr11:65558200-65560800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:65558200-65561800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:65558200-65562600	Genic enhancers	Fetal Intestine Small	intestine
39	chr11:65558200-65564800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr11:65558200-65568800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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