Variant report

Variant	rs10121699
Chromosome Location	chr9:79029798-79029799
allele	C/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	MYC	chr9:79029644-79029870	MCF10A-Er-Src	breast:	n/a	n/a
2	YY1	chr9:79029463-79029882	GM12878	blood:	n/a	n/a
3	RUNX3	chr9:79029440-79029960	GM12878	blood:	n/a	n/a
4	RUNX3	chr9:79029451-79029968	GM12878	blood:	n/a	n/a
5	STAT3	chr9:79029563-79029864	MCF10A-Er-Src	breast:	n/a	n/a
6	CREB1	chr9:79029552-79030006	GM12878	blood:	n/a	n/a
7	YY1	chr9:79029443-79029875	GM12891	blood:	n/a	n/a
8	POU2F2	chr9:79029379-79029887	GM12878	blood:	n/a	n/a
9	FOS	chr9:79029506-79030918	HUVEC	blood vessel:	n/a	chr9:79030251-79030262 chr9:79030647-79030659
10	FOS	chr9:79029606-79030446	MCF10A-Er-Src	breast:	n/a	chr9:79030251-79030262
11	SPI1	chr9:79029502-79029869	GM12878	blood:	n/a	n/a
12	SPI1	chr9:79029446-79029839	GM12891	blood:	n/a	n/a
13	STAT3	chr9:79029665-79029867	MCF10A-Er-Src	breast:	n/a	n/a
14	EP300	chr9:79029618-79029875	GM12878	blood:	n/a	n/a
15	YY1	chr9:79029487-79029894	GM12878	blood:	n/a	n/a
16	FOS	chr9:79029609-79030990	MCF10A-Er-Src	breast:	n/a	chr9:79030251-79030262 chr9:79030647-79030659
17	CREB1	chr9:79029495-79029997	GM12878	blood:	n/a	n/a
18	GATA2	chr9:79029638-79029973	HUVEC	blood vessel:	n/a	n/a
19	SPI1	chr9:79029553-79029835	GM12891	blood:	n/a	n/a
20	YY1	chr9:79029584-79029881	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79008306..79010986-chr9:79027857..79030537,2	MCF-7	breast:

Variant related genes	Relation type
GCNT1	TF binding region
ENSG00000135002	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10114264	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10124695	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10735646	0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs10781362	0.82[ASN][1000 genomes]
rs10869767	0.84[ASN][1000 genomes]
rs10869773	0.86[ASN][1000 genomes]
rs10869780	0.85[EUR][1000 genomes]
rs11144864	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs11144865	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs11144871	0.82[ASN][1000 genomes]
rs11144880	0.85[ASN][1000 genomes]
rs11144899	0.82[ASN][1000 genomes]
rs11788095	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12057052	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13288968	0.88[ASN][1000 genomes]
rs13295433	0.86[ASN][1000 genomes]
rs1535845	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1961995	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs2002423	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251604	0.82[ASN][1000 genomes]
rs2377639	0.95[JPT][hapmap]
rs2490572	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2490574	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2490576	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2490579	0.82[ASN][1000 genomes]
rs2490583	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2490584	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2490586	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501920	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501922	0.80[ASN][1000 genomes]
rs2501923	0.82[ASN][1000 genomes]
rs2501925	0.84[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2501927	0.82[ASN][1000 genomes]
rs2501930	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501932	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2501937	0.86[ASN][1000 genomes]
rs2501938	0.86[ASN][1000 genomes]
rs2501939	0.87[ASN][1000 genomes]
rs2501940	0.84[EUR][1000 genomes]
rs2501942	0.85[EUR][1000 genomes]
rs3739729	0.82[ASN][1000 genomes]
rs4372070	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs4745541	0.81[ASN][1000 genomes]
rs4745544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4745545	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4745546	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4745548	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6560517	0.86[ASN][1000 genomes]
rs6560519	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6560520	0.83[ASN][1000 genomes]
rs6560521	0.83[ASN][1000 genomes]
rs6560522	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7847608	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7849239	0.86[ASN][1000 genomes]
rs7861089	0.86[ASN][1000 genomes]

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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv3451027	chr9:79021447-79056132	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10121699	C9orf40	cis	cerebellum	SCAN
rs10121699	ZSWIM4	trans	brain	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79027600-79029800	ZNF genes & repeats	GM12878-XiMat	blood
2	chr9:79029000-79031600	Enhancers	HUVEC	blood vessel
3	chr9:79029200-79031200	Enhancers	NH-A	brain
4	chr9:79029200-79031400	Enhancers	Hela-S3	cervix
5	chr9:79029400-79030200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr9:79029600-79029800	Enhancers	H9 Cell Line	embryonic stem cell
7	chr9:79029600-79030200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:79029600-79030200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr9:79029600-79030400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:79029600-79031200	Enhancers	Osteobl	bone
11	chr9:79029600-79031400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:79029600-79031600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:79029600-79032800	Enhancers	Stomach Mucosa	stomach

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