Variant report

Variant	rs7551777
Chromosome Location	chr1:62675709-62675710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr1:62675363-62677428	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD2	chr1:62675567-62679535	H1-hESC	embryonic stem cell:	n/a	n/a
3	SMC3	chr1:62675660-62676329	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:62675402-62677410	H1-hESC	embryonic stem cell:	n/a	n/a
5	ATF2	chr1:62675552-62677433	H1-hESC	embryonic stem cell:	n/a	n/a
6	GTF2F1	chr1:62675517-62679496	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:62675505-62676298	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:62671110-62680443	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:62675548-62675915	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF7	chr1:62675465-62677366	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr1:62675410-62676375	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:62672294-62680406	H1-hESC	embryonic stem cell:	n/a	n/a
13	USF2	chr1:62675641-62677196	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUND	chr1:62675640-62675784	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000237227	TF binding region
ENSG00000200174	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10889296	1.00[CEU][hapmap]
rs10889298	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10889299	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10889300	0.83[ASN][1000 genomes]
rs11207924	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11207925	0.83[ASN][1000 genomes]
rs11207926	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11207930	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207931	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207933	0.83[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11207936	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803019	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806202	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809029	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123184	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41514144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs56011715	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59949671	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74079019	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539677	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv870842	chr1:62644118-62679202	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7551777	CNPY1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62664800-62677800	Weak transcription	Placenta	Placenta
2	chr1:62666000-62695400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:62667400-62676200	Strong transcription	Placenta Amnion	Placenta Amnion
4	chr1:62668400-62677200	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr1:62670400-62677200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:62670600-62676200	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:62671800-62678200	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr1:62672200-62677400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
9	chr1:62673200-62676400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:62673800-62677200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
11	chr1:62673800-62677200	ZNF genes & repeats	Fetal Lung	lung
12	chr1:62674000-62677200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:62674400-62676800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
14	chr1:62674400-62678800	Weak transcription	Colonic Mucosa	Colon
15	chr1:62674600-62675800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:62674600-62676000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:62675000-62676400	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:62675400-62676000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:62675400-62676000	Enhancers	NHEK	skin
20	chr1:62675400-62676200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:62675400-62676200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:62675400-62676400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr1:62675400-62676400	Enhancers	HSMM	muscle
24	chr1:62675400-62676800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:62675400-62677000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr1:62675400-62677000	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr1:62675600-62675800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr1:62675600-62675800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:62675600-62675800	ZNF genes & repeats	Fetal Kidney	kidney
30	chr1:62675600-62675800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
31	chr1:62675600-62676200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:62675600-62676200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:62675600-62676200	ZNF genes & repeats	Fetal Stomach	stomach
34	chr1:62675600-62676200	ZNF genes & repeats	Right Atrium	heart
35	chr1:62675600-62676200	Enhancers	HMEC	breast
36	chr1:62675600-62676400	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr1:62675600-62676400	Enhancers	Hela-S3	cervix
38	chr1:62675600-62676400	Enhancers	HSMMtube	muscle
39	chr1:62675600-62677200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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