Variant report

Variant	rs7324024
Chromosome Location	chr13:50161512-50161513
allele	C/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	NFIC	chr13:50161202-50162028	HepG2	liver:	n/a	n/a
2	FOXA1	chr13:50161188-50162020	HepG2	liver:	n/a	chr13:50161818-50161830
3	JUND	chr13:50161489-50161856	HepG2	liver:	n/a	n/a
4	FOS	chr13:50161056-50161771	MCF10A-Er-Src	breast:	n/a	n/a
5	RCOR1	chr13:50160917-50161956	IMR90	lung:	n/a	n/a
6	FOXA1	chr13:50161285-50162130	HepG2	liver:	n/a	chr13:50161818-50161830
7	BHLHE40	chr13:50161385-50162070	HepG2	liver:	n/a	n/a
8	STAT3	chr13:50160886-50161761	MCF10A-Er-Src	breast:	n/a	n/a
9	MYBL2	chr13:50161433-50162040	HepG2	liver:	n/a	n/a
10	SP1	chr13:50161417-50162057	HepG2	liver:	n/a	n/a
11	HDAC2	chr13:50161274-50161975	HepG2	liver:	n/a	chr13:50161751-50161765 chr13:50161830-50161844 chr13:50161752-50161766
12	MAX	chr13:50161360-50161834	HepG2	liver:	n/a	n/a
13	TEAD4	chr13:50161261-50162113	HepG2	liver:	n/a	chr13:50161609-50161618
14	FOXA1	chr13:50160755-50162015	HepG2	liver:	n/a	chr13:50160757-50160769 chr13:50161818-50161830
15	ARID3A	chr13:50161361-50161950	HepG2	liver:	n/a	n/a
16	FOS	chr13:50161341-50161674	MCF10A-Er-Src	breast:	n/a	n/a
17	MYC	chr13:50161420-50161613	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr13:50160985-50161761	MCF10A-Er-Src	breast:	n/a	n/a
19	FOS	chr13:50161088-50161742	MCF10A-Er-Src	breast:	n/a	n/a
20	FOXA2	chr13:50161280-50162009	HepG2	liver:	n/a	chr13:50161818-50161830
21	MYBL2	chr13:50161391-50162081	HepG2	liver:	n/a	n/a
22	NFIC	chr13:50161386-50161937	HepG2	liver:	n/a	n/a
23	FOS	chr13:50161357-50161689	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr13:50160738-50161761	MCF10A-Er-Src	breast:	n/a	n/a
25	EP300	chr13:50161240-50162039	HepG2	liver:	n/a	n/a
26	FOXA2	chr13:50161059-50162129	HepG2	liver:	n/a	chr13:50161818-50161830
27	TCF7L2	chr13:50161253-50161957	HepG2	liver:	n/a	n/a
28	FOXA1	chr13:50161293-50162068	HepG2	liver:	n/a	chr13:50161818-50161830
29	MBD4	chr13:50161274-50162048	HepG2	liver:	n/a	n/a
30	MYC	chr13:50161310-50161719	MCF10A-Er-Src	breast:	n/a	n/a
31	EP300	chr13:50161304-50161926	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:50087217..50089138-chr13:50160277..50162233,2	MCF-7	breast:
2	chr13:50158705..50160311-chr13:50160787..50163577,2	K562	blood:
3	chr13:50016508..50019619-chr13:50158297..50162493,5	MCF-7	breast:
4	chr13:50018091..50020783-chr13:50160403..50162609,2	MCF-7	breast:
5	chr13:50091935..50095583-chr13:50159811..50161648,3	MCF-7	breast:

Variant related genes	Relation type
RCBTB1	TF binding region
ENSG00000136144	Chromatin interaction
ENSG00000102547	Chromatin interaction
ENSG00000136169	Chromatin interaction
ENSG00000215462	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1198421	0.98[ASN][1000 genomes]
rs1198422	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1359542	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536192	0.86[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1536195	0.86[EUR][1000 genomes]
rs1570883	0.85[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs1886793	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1998780	0.85[CEU][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1998781	0.85[CEU][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2104183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209506	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2274278	0.85[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs2274284	0.86[ASW][hapmap];0.85[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2407697	0.85[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs2897741	0.81[EUR][1000 genomes]
rs3794376	0.85[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4572288	0.90[ASN][1000 genomes]
rs4941648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941650	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5007254	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561539	0.82[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs6561540	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6561542	0.90[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs7139724	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7317140	0.85[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs7983283	0.83[EUR][1000 genomes]
rs7986405	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7989286	0.87[EUR][1000 genomes]
rs7992691	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7994516	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7996012	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8000962	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526577	0.80[CEU][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535259	0.85[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs9535262	0.85[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9535269	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562896	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9596161	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1046912	chr13:50122840-50189313	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv1043902	chr13:50122840-50189999	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
13	esv2761789	chr13:50122852-50185910	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv455883	chr13:50124621-50185204	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv561617	chr13:50124621-50185204	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
17	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7324024	ARL11	Cis_1M	lymphoblastoid	RTeQTL
rs7324024	CAB39L	cis	cerebellum	SCAN
rs7324024	RCBTB1	cis	cerebellum	SCAN
rs7324024	ARL11	cis	parietal	SCAN
rs7324024	CYSLTR2	cis	cerebellum	SCAN
rs7324024	RCBTB1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50160400-50161800	Enhancers	Muscle Satellite Cultured Cells	--
2	chr13:50160400-50161800	Flanking Active TSS	HepG2	liver
3	chr13:50160400-50161800	Enhancers	HSMMtube	muscle
4	chr13:50160400-50161800	Enhancers	NHLF	lung
5	chr13:50160400-50161800	Enhancers	Osteobl	bone
6	chr13:50160400-50162000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:50160400-50162200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr13:50160600-50161600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:50160600-50161600	Enhancers	Liver	Liver
10	chr13:50160600-50161600	Enhancers	A549	lung
11	chr13:50160600-50161600	Weak transcription	K562	blood
12	chr13:50160600-50161800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:50160600-50161800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr13:50160600-50161800	Enhancers	HUVEC	blood vessel
15	chr13:50160600-50162000	Enhancers	Hela-S3	cervix
16	chr13:50160600-50162400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr13:50160600-50162400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr13:50160600-50162400	Enhancers	HMEC	breast
19	chr13:50160600-50162600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr13:50160600-50169200	Weak transcription	Esophagus	oesophagus
21	chr13:50161000-50161600	Weak transcription	Fetal Heart	heart
22	chr13:50161000-50161800	Enhancers	NH-A	brain
23	chr13:50161000-50161800	Flanking Active TSS	NHEK	skin
24	chr13:50161200-50161600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr13:50161400-50161600	Enhancers	Psoas Muscle	Psoas
26	chr13:50161400-50161800	Enhancers	HSMM	muscle

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