Variant report

Variant	rs12000794
Chromosome Location	chr9:103157515-103157516
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr9:103157424-103157568	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr9:103157440-103157590	A549	lung:	n/a	n/a
3	CTCF	chr9:103157460-103157610	HPAF	blood vessel:	n/a	n/a
4	RAD21	chr9:103157356-103157625	HepG2	liver:	n/a	n/a
5	RAD21	chr9:103157364-103157680	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr9:103157380-103157655	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr9:103157469-103157571	GM12878	blood:	n/a	n/a
8	CTCF	chr9:103157470-103157551	ProgFib	skin:	n/a	n/a
9	CTCF	chr9:103157460-103157610	HEK293	kidney:	n/a	n/a
10	CTCF	chr9:103157497-103157585	A549	lung:	n/a	n/a
11	CTCF	chr9:103157430-103157623	Gliobla	brain:	n/a	n/a
12	MAX	chr9:103157494-103157562	NB4	blood:	n/a	n/a
13	CTCF	chr9:103157438-103157613	NHEK	skin:	n/a	n/a
14	CTCF	chr9:103157455-103157595	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr9:103157480-103157630	HPAF	blood vessel:	n/a	n/a
16	CTCF	chr9:103157485-103157571	MCF-7	breast:	n/a	n/a
17	CTCF	chr9:103157460-103157610	HCPEpiC	choroid plexus:	n/a	n/a
18	RAD21	chr9:103157330-103157755	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr9:103157310-103157632	A549	lung:	n/a	n/a
20	CTCF	chr9:103157462-103157569	HepG2	liver:	n/a	n/a
21	CTCF	chr9:103157400-103157550	HBMEC	blood vessel:	n/a	n/a
22	RAD21	chr9:103157362-103157602	HepG2	liver:	n/a	n/a
23	CTCF	chr9:103157368-103157665	GM12878	blood:	n/a	n/a
24	CTCF	chr9:103157483-103157563	Fibrobl	skin:	n/a	n/a
25	CTCF	chr9:103157440-103157590	WERI-Rb-1	eye:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000263475	TF binding region

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10819755	0.86[CEU][hapmap]
rs10819758	0.91[CEU][hapmap];0.90[GIH][hapmap]
rs10819771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989046	0.82[CEU][hapmap]
rs10989047	0.91[CEU][hapmap]
rs10989051	0.91[CEU][hapmap];0.90[GIH][hapmap]
rs10989072	0.91[CEU][hapmap];0.90[GIH][hapmap]
rs10989073	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989075	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989077	0.86[EUR][1000 genomes]
rs11790067	0.82[AMR][1000 genomes]
rs11790431	0.82[CEU][hapmap];0.90[GIH][hapmap]
rs12002124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375859	0.83[EUR][1000 genomes]
rs12378432	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13284601	1.00[CHB][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919024	0.82[CEU][hapmap];0.90[GIH][hapmap]
rs2039396	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2039397	1.00[ASN][1000 genomes]
rs7027939	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029342	0.89[CEU][hapmap]
rs7039994	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs7849019	0.91[CEU][hapmap]
rs944942	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12000794	CYLC2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103151800-103160000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:103154000-103158000	Weak transcription	Left Ventricle	heart
3	chr9:103156200-103157600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:103156400-103157600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:103156800-103158000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr9:103157000-103157600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:103157000-103157600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:103157000-103157600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:103157000-103157600	Enhancers	Osteobl	bone
10	chr9:103157000-103157800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr9:103157000-103158200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr9:103157000-103158200	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr9:103157000-103158600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:103157200-103157800	Enhancers	Primary hematopoietic stem cells	blood
15	chr9:103157200-103159000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:103157400-103157600	Enhancers	A549	lung

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