Variant report

Variant	rs1455954
Chromosome Location	chr11:5000043-5000044
allele	C/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	11:4988858-5002113..11:5243048-5250847	Hela-S3	cervix:
2	11:4988858-5002113..11:5566274-5571131	Hela-S3	cervix:
3	11:4940074-4947279..11:4988858-5002113	Hela-S3	cervix:
4	11:4988858-5002113..11:5505728-5514500	Hela-S3	cervix:
5	11:4988858-5002113..11:5700314-5707362	Hela-S3	cervix:
6	11:4988858-5002113..11:5250847-5268367	Hela-S3	cervix:
7	11:4988858-5002113..11:5527719-5533869	Hela-S3	cervix:
8	chr11:4998734..5001673-chr11:5002692..5004874,2	MCF-7	breast:
9	11:4789513-4794705..11:4988858-5002113	Hela-S3	cervix:
10	11:4988858-5002113..11:5600743-5604452	Hela-S3	cervix:
11	11:4778081-4789138..11:4988858-5002113	Hela-S3	cervix:
12	11:4988858-5002113..11:5721056-5732713	Hela-S3	cervix:
13	11:4988858-5002113..11:5469844-5475173	Hela-S3	cervix:
14	11:4988858-5002113..11:5707362-5712027	Hela-S3	cervix:
15	11:4988858-5002113..11:5714465-5718134	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000132256	Chromatin interaction
ENSG00000132274	Chromatin interaction
ENSG00000221031	Chromatin interaction
ENSG00000229988	Chromatin interaction
ENSG00000223609	Chromatin interaction
ENSG00000181609	Chromatin interaction
ENSG00000167346	Chromatin interaction
ENSG00000260629	Chromatin interaction
ENSG00000188069	Chromatin interaction
ENSG00000187747	Chromatin interaction
ENSG00000244734	Chromatin interaction
ENSG00000187918	Chromatin interaction
ENSG00000175520	Chromatin interaction
ENSG00000176879	Chromatin interaction
ENSG00000181616	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10082653	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10734457	0.85[CEU][hapmap]
rs10734458	0.85[CEU][hapmap]
rs10734468	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs10768406	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10768424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10768434	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs10837037	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11034913	0.81[CEU][hapmap]
rs11034915	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11034931	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11034951	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11034955	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1368820	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1368821	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1368822	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1378738	0.81[CEU][hapmap]
rs1598507	0.84[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1598508	0.83[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4910694	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6578538	0.83[EUR][1000 genomes]
rs7104839	0.96[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7107374	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7108624	0.96[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7123513	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7123673	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9651651	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	esv2758254	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv2759799	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv1054610	chr11:4953844-5004203	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	nsv526998	chr11:4954607-5074301	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1045154	chr11:4958462-5032685	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv540937	chr11:4958462-5032685	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1046693	chr11:4958462-5177455	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv540938	chr11:4958462-5177455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
10	nsv896918	chr11:4960032-5001570	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
11	esv2760169	chr11:4961518-5233821	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
12	nsv1041662	chr11:4967061-5001831	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
13	nsv1037991	chr11:4983908-5036608	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv540939	chr11:4983908-5036608	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv972943	chr11:4993946-5001630	Weak transcription Enhancers	TF binding region Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1455954	LSP1	cis	cerebellum	SCAN
rs1455954	OR52N1	cis	cerebellum	SCAN
rs1455954	GVIN1	cis	parietal	SCAN
rs1455954	OR51G2	cis	parietal	SCAN
rs1455954	SYT8	cis	parietal	SCAN
rs1455954	OLFML1	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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