Variant report

Variant	rs7107912
Chromosome Location	chr11:65603252-65603253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65601147..65603673-chr11:65623876..65625928,3	MCF-7	breast:
2	chr11:65599027..65600852-chr11:65601394..65604291,2	K562	blood:

Variant related genes	Relation type
ENSG00000172732	Chromatin interaction
ENSG00000172757	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10750772	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10791827	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896047	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10896051	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10896052	0.90[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10896061	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896064	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11227309	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11227311	0.90[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11227312	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227318	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11602769	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12575663	0.92[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12576996	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs13817	0.86[GIH][hapmap]
rs1939212	0.82[GIH][hapmap]
rs35083694	0.84[ASN][1000 genomes]
rs3892696	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap]
rs3903072	0.81[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs485036	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs4930320	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4930326	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs501630	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs558114	0.84[GIH][hapmap]
rs566266	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs570387	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs575631	0.85[ASN][1000 genomes]
rs589253	0.81[MEX][hapmap]
rs594689	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs617791	0.81[MEX][hapmap]
rs630303	0.84[GIH][hapmap]
rs633800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635375	0.84[GIH][hapmap]
rs648732	0.84[GIH][hapmap]
rs652021	0.84[GIH][hapmap]
rs656040	0.86[GIH][hapmap]
rs659824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs659857	0.84[GIH][hapmap]
rs665306	0.84[GIH][hapmap]
rs668356	0.84[GIH][hapmap]
rs674126	0.88[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs677029	0.81[MEX][hapmap]
rs7123155	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs875311	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
2	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
3	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
7	nsv555215	chr11:65581579-65676516	Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
8	esv3328198	chr11:65600476-65603674	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv3364341	chr11:65600476-65603674	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7107912	EFEMP2	cis	cerebellum	SCAN
rs7107912	SNX32	cis	Thyroid	GTEx
rs7107912	PACS1	cis	parietal	SCAN
rs7107912	RAB1B	cis	cerebellum	SCAN
rs7107912	EIF1AD	cis	parietal	SCAN
rs7107912	PRDX5	cis	parietal	SCAN
rs7107912	CARNS1	cis	cerebellum	SCAN
rs7107912	SART1	cis	parietal	SCAN
rs7107912	PLCB3	cis	parietal	SCAN
rs7107912	SNX32	cis	parietal	SCAN
rs7107912	SNX32	cis	Whole Blood	GTEx
rs7107912	SNX32	cis	cerebellum	SCAN
rs7107912	LRRN4CL	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65602200-65611000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:65602200-65618800	Weak transcription	Colonic Mucosa	Colon
3	chr11:65602200-65619000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:65602200-65623800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:65602400-65605000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:65602400-65611400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:65602400-65618200	Weak transcription	Primary B cells from cord blood	blood
8	chr11:65602400-65618400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:65602600-65603400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:65602600-65611200	Weak transcription	Fetal Intestine Small	intestine
11	chr11:65602600-65618600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:65602800-65603400	Active TSS	Fetal Brain Female	brain
13	chr11:65602800-65618800	Weak transcription	Brain Anterior Caudate	brain
14	chr11:65603200-65603400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:65603200-65603600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:65603200-65617400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:65603200-65618000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links