Variant report

Variant	rs878545
Chromosome Location	chr11:17555590-17555591
allele	A/G
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	CREB1	chr11:17555309-17555642	H1-hESC	embryonic stem cell:	n/a	n/a
2	CREB1	chr11:17555365-17555768	H1-hESC	embryonic stem cell:	n/a	n/a
3	RFX5	chr11:17555358-17555720	Hela-S3	cervix:	n/a	n/a
4	TCF7L2	chr11:17555322-17555810	Hela-S3	cervix:	n/a	n/a
5	SMC3	chr11:17555375-17555757	Hela-S3	cervix:	n/a	n/a
6	MAFK	chr11:17555277-17555908	Hela-S3	cervix:	n/a	n/a
7	CHD2	chr11:17555320-17555729	Hela-S3	cervix:	n/a	n/a
8	MAX	chr11:17555359-17555676	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr11:17555460-17555660	H1-hESC	embryonic stem cell:	n/a	n/a
10	EP300	chr11:17555374-17555703	Hela-S3	cervix:	n/a	chr11:17555565-17555572
11	TFAP2C	chr11:17555248-17555793	Hela-S3	cervix:	n/a	n/a
12	JUND	chr11:17555435-17555624	HepG2	liver:	n/a	n/a
13	CEBPB	chr11:17555310-17555766	Hela-S3	cervix:	n/a	n/a
14	SMARCC1	chr11:17555236-17555968	Hela-S3	cervix:	n/a	n/a
15	MAZ	chr11:17555339-17555785	Hela-S3	cervix:	n/a	n/a
16	RCOR1	chr11:17555337-17555697	Hela-S3	cervix:	n/a	n/a
17	BRCA1	chr11:17555340-17555781	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
USH1C	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12270598	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12272861	0.80[AMR][1000 genomes]
rs12273896	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12275068	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16934376	0.85[JPT][hapmap]
rs2355021	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41282940	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4756899	1.00[YRI][hapmap]
rs7112757	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72870321	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72870323	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72870330	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs733126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs886817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs878545	SOX6	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine
2	chr11:17541600-17555800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:17547200-17563200	Genic enhancers	Fetal Intestine Small	intestine
4	chr11:17551600-17556200	Genic enhancers	Fetal Intestine Large	intestine
5	chr11:17553600-17557000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:17553600-17557200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:17553600-17561800	Weak transcription	Gastric	stomach
8	chr11:17553600-17562200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:17553800-17556600	Weak transcription	Brain Anterior Caudate	brain
10	chr11:17553800-17556800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:17553800-17558200	Weak transcription	Stomach Mucosa	stomach
12	chr11:17553800-17558600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:17553800-17563200	Weak transcription	Colonic Mucosa	Colon
14	chr11:17554600-17556000	Flanking Active TSS	Hela-S3	cervix
15	chr11:17554800-17555600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr11:17554800-17555800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr11:17554800-17556000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:17555000-17556200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr11:17555200-17555600	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr11:17555200-17555800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr11:17555400-17555800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:17555400-17560400	Weak transcription	Duodenum Mucosa	Duodenum

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