Variant report

Variant	rs4646823
Chromosome Location	chr11:67434416-67434417
allele	G/T
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	CTCF	chr11:67434360-67434510	GM12872	blood:	n/a	chr11:67434412-67434420
2	CTCF	chr11:67434300-67434450	HepG2	liver:	n/a	chr11:67434412-67434420
3	CTCF	chr11:67434300-67434450	HMEC	breast:	n/a	chr11:67434412-67434420
4	CTCF	chr11:67434280-67434430	MCF-7	breast:	n/a	chr11:67434412-67434420
5	CTCF	chr11:67434320-67434470	HEK293	kidney:	n/a	chr11:67434412-67434420
6	CTCF	chr11:67434300-67434450	GM12873	blood:	n/a	chr11:67434412-67434420
7	CTCF	chr11:67434280-67434430	GM12872	blood:	n/a	chr11:67434412-67434420
8	CTCF	chr11:67434320-67434470	GM12875	blood:	n/a	chr11:67434412-67434420
9	CTCF	chr11:67434300-67434450	SAEC	small airway:	n/a	chr11:67434412-67434420
10	CTCF	chr11:67434320-67434470	NHEK	skin:	n/a	chr11:67434412-67434420
11	EBF1	chr11:67434236-67434796	GM12878	blood:	n/a	chr11:67434620-67434629 chr11:67434618-67434631 chr11:67434618-67434629 chr11:67434619-67434629
12	CTCF	chr11:67434280-67434430	Hela-S3	cervix:	n/a	chr11:67434412-67434420

No.	Distal block	Cell Line	Cell type
1	chr11:67433386..67435111-chr11:67439487..67442786,3	MCF-7	breast:
2	chr11:67433174..67435037-chr11:67457178..67460056,2	MCF-7	breast:
3	chr11:67380317..67383233-chr11:67433739..67435714,2	MCF-7	breast:
4	chr11:67434114..67434965-chr11:67458274..67458971,2	MCF-7	breast:

Variant related genes	Relation type
ALDH3B2	TF binding region
ENSG00000132746	Chromatin interaction
ENSG00000231793	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10736660	0.87[GIH][hapmap];0.86[MEX][hapmap]
rs11601010	0.96[EUR][1000 genomes]
rs11603033	0.82[CHB][hapmap]
rs11828473	0.95[EUR][1000 genomes]
rs1551886	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1551888	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17510687	0.80[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs17856219	0.97[EUR][1000 genomes]
rs1903829	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs1979375	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1979376	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2054409	0.89[YRI][hapmap]
rs2126716	0.96[EUR][1000 genomes]
rs2252577	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs2447597	0.85[GIH][hapmap]
rs2447598	0.80[AMR][1000 genomes]
rs2509718	0.97[EUR][1000 genomes]
rs2509719	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2514024	0.85[GIH][hapmap]
rs2885171	0.85[GIH][hapmap];0.83[YRI][hapmap]
rs3127	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3741172	0.97[EUR][1000 genomes]
rs3888976	0.95[EUR][1000 genomes]
rs4520603	0.91[EUR][1000 genomes]
rs4930211	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4930212	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4930465	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61894521	0.96[EUR][1000 genomes]
rs61894522	0.96[EUR][1000 genomes]
rs61894523	0.96[EUR][1000 genomes]
rs61894524	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61894527	0.91[EUR][1000 genomes]
rs61894528	0.91[EUR][1000 genomes]
rs6591267	0.85[GIH][hapmap];0.83[YRI][hapmap]
rs7127140	0.97[EUR][1000 genomes]
rs7947978	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes]
rs866907	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948445	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	esv2422195	chr11:67234322-67626901	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
3	nsv1041988	chr11:67319916-67749246	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv897814	chr11:67339949-67460529	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1050463	chr11:67343421-67717338	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1038189	chr11:67345320-67749246	Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv1047236	chr11:67345320-67764068	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
8	nsv555268	chr11:67346743-67752972	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
9	nsv1036101	chr11:67346813-67828351	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
10	nsv541079	chr11:67346813-67828351	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic 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 miRNA target site	139 gene(s)	inside rSNPs	diseases
11	nsv1053811	chr11:67349444-67749246	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
12	esv1817852	chr11:67349899-67626567	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
13	nsv468606	chr11:67352689-67816936	Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
14	nsv555269	chr11:67352689-67816936	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
15	nsv897816	chr11:67353579-67460529	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
16	nsv1041887	chr11:67357365-67464893	Flanking Active TSS Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
17	nsv541080	chr11:67357365-67464893	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
18	nsv529452	chr11:67358204-67465721	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
19	nsv492253	chr11:67358204-67574402	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
20	nsv1043487	chr11:67360899-67662476	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
21	nsv897820	chr11:67372477-67460529	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
22	nsv897822	chr11:67378594-67441553	Genic enhancers Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
23	nsv897823	chr11:67378594-67460529	Enhancers Bivalent Enhancer Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
24	nsv897825	chr11:67381110-67460529	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
25	nsv469963	chr11:67395714-67438195	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
26	nsv897826	chr11:67408791-67462549	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
27	esv1812708	chr11:67414492-67441553	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
28	nsv555274	chr11:67433869-67752972	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4646823	LRP5	cis	cerebellum	SCAN
rs4646823	HRASLS2	cis	cerebellum	SCAN
rs4646823	DPP3	cis	parietal	SCAN
rs4646823	BRMS1	cis	cerebellum	SCAN
rs4646823	ZFPL1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67430600-67440800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:67430800-67435200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:67431200-67437800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:67433200-67435400	Enhancers	Fetal Thymus	thymus
5	chr11:67433400-67436600	Enhancers	Primary B cells from peripheral blood	blood
6	chr11:67433600-67435400	Enhancers	Primary B cells from cord blood	blood
7	chr11:67433800-67434600	Enhancers	Dnd41	blood
8	chr11:67434000-67435000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:67434000-67442400	Weak transcription	Fetal Intestine Small	intestine
10	chr11:67434200-67435800	Enhancers	GM12878-XiMat	blood
11	chr11:67434200-67436000	Enhancers	Spleen	Spleen
12	chr11:67434400-67435800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:67434400-67436600	Weak transcription	Esophagus	oesophagus
14	chr11:67434400-67438600	Enhancers	Placenta	Placenta

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