Variant report

Variant	rs62438733
Chromosome Location	chr7:11287944-11287945
allele	A/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	chr7:11287914-11288162	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr7:11287899-11288171	MCF10A-Er-Src	breast:	n/a	n/a
3	ZNF217	chr7:11287836-11288194	MCF-7	breast:	n/a	n/a
4	GABPA	chr7:11287766-11288230	MCF-7	breast:	n/a	n/a
5	NR2F2	chr7:11287735-11288333	MCF-7	breast:	n/a	n/a
6	FOXA1	chr7:11287831-11288173	HepG2	liver:	n/a	chr7:11288066-11288081
7	FOSL2	chr7:11287743-11288191	MCF-7	breast:	n/a	chr7:11287846-11287853
8	FOXA1	chr7:11287804-11288151	HepG2	liver:	n/a	chr7:11288066-11288081
9	FOXA2	chr7:11287852-11288180	HepG2	liver:	n/a	n/a
10	MAX	chr7:11287867-11288201	HepG2	liver:	n/a	n/a
11	FOXA2	chr7:11287839-11288192	A549	lung:	n/a	n/a
12	ARID3A	chr7:11287818-11288185	HepG2	liver:	n/a	n/a
13	GATA3	chr7:11287910-11288003	MCF-7	breast:	n/a	n/a
14	JUND	chr7:11287803-11288180	MCF-7	breast:	n/a	chr7:11287846-11287853 chr7:11287980-11287991
15	GATA3	chr7:11287872-11288207	T-47D	breast:	n/a	n/a
16	TCF7L2	chr7:11287912-11288193	MCF-7	breast:	n/a	n/a
17	FOXA1	chr7:11287859-11288275	T-47D	breast:	n/a	chr7:11288066-11288081
18	CEBPB	chr7:11287633-11287947	HepG2	liver:	n/a	chr7:11287751-11287762
19	FOXA1	chr7:11287890-11288142	HepG2	liver:	n/a	chr7:11288066-11288081
20	FOSL2	chr7:11287720-11288241	MCF-7	breast:	n/a	chr7:11287846-11287853
21	NR2F2	chr7:11287788-11288151	MCF-7	breast:	n/a	n/a
22	SRF	chr7:11287644-11288361	MCF-7	breast:	n/a	n/a
23	JUND	chr7:11287852-11288123	HepG2	liver:	n/a	chr7:11287980-11287991
24	HDAC2	chr7:11287755-11288203	MCF-7	breast:	n/a	chr7:11287820-11287834
25	CEBPB	chr7:11287597-11288246	MCF-7	breast:	n/a	chr7:11287751-11287762
26	FOXA1	chr7:11287805-11288184	HepG2	liver:	n/a	chr7:11288066-11288081
27	FOXA1	chr7:11287844-11288156	T-47D	breast:	n/a	chr7:11288066-11288081
28	MAX	chr7:11287881-11288310	MCF-7	breast:	n/a	n/a
29	GATA3	chr7:11287690-11288355	MCF-7	breast:	n/a	n/a
30	FOS	chr7:11287902-11288124	MCF10A-Er-Src	breast:	n/a	n/a
31	JUND	chr7:11287727-11288160	MCF-7	breast:	n/a	chr7:11287846-11287853 chr7:11287980-11287991
32	FOSL2	chr7:11287848-11288204	HepG2	liver:	n/a	n/a
33	GATA3	chr7:11287693-11288405	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:11287653..11289211-chr7:11291988..11294174,2	MCF-7	breast:
2	chr7:11252043..11254339-chr7:11287708..11289525,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHF14-1	chr7:11287920-11288002	ENSG00000230333.1

Variant related genes	Relation type
ENSG00000230333	TF binding region
ENSG00000230333	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10259746	0.93[EUR][1000 genomes]
rs10275065	0.93[EUR][1000 genomes]
rs10440999	0.86[EUR][1000 genomes]
rs11766955	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768674	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11768679	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11768917	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11770592	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978019	0.83[EUR][1000 genomes]
rs12111845	0.91[EUR][1000 genomes]
rs1557859	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17164110	0.93[EUR][1000 genomes]
rs17164121	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17164129	0.99[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs17164130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353796	0.96[EUR][1000 genomes]
rs2353797	0.96[EUR][1000 genomes]
rs2353800	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353805	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2883284	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2883285	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377852	0.96[EUR][1000 genomes]
rs4377853	0.96[EUR][1000 genomes]
rs4639408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56087423	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62438728	0.96[EUR][1000 genomes]
rs62438729	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62438732	0.80[AFR][1000 genomes]
rs7456811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792979	0.99[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7793119	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793413	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7794576	0.96[EUR][1000 genomes]
rs7795098	0.90[EUR][1000 genomes]
rs7798550	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[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	nsv1067780	chr7:10649696-11329787	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv491695	chr7:10649696-11329787	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1019888	chr7:10712858-11496785	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1029836	chr7:10713523-11492751	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv538730	chr7:10713523-11492751	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv532092	chr7:10731350-11414759	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv1024171	chr7:10810444-11559156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv1029882	chr7:10872162-11371145	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv817291	chr7:10875417-11562683	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv428162	chr7:11085784-11359333	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv523279	chr7:11198193-11473561	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv518180	chr7:11198193-11475819	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1015837	chr7:11208733-11475112	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv538732	chr7:11208733-11475112	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1028326	chr7:11221209-11754436	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv538733	chr7:11221209-11754436	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv1024940	chr7:11276392-11310923	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:11277000-11292600	Weak transcription	Stomach Mucosa	stomach
2	chr7:11277800-11291600	Weak transcription	Liver	Liver
3	chr7:11277800-11293800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:11277800-11305400	Weak transcription	Adipose Nuclei	Adipose
5	chr7:11287800-11288000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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