Variant report

Variant	rs3757481
Chromosome Location	chr7:6748260-6748261
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	MAFK	chr7:6747938-6748266	HepG2	liver:	n/a	chr7:6748072-6748086
2	FOXA1	chr7:6747923-6748297	HepG2	liver:	n/a	n/a
3	SP1	chr7:6747864-6748354	HepG2	liver:	n/a	n/a
4	FOXA1	chr7:6747807-6748419	HepG2	liver:	n/a	n/a
5	MAFF	chr7:6747871-6748272	HepG2	liver:	n/a	chr7:6748071-6748089
6	FOXA1	chr7:6747878-6748411	HepG2	liver:	n/a	n/a
7	FOXA1	chr7:6747852-6748412	HepG2	liver:	n/a	n/a
8	HNF4G	chr7:6747923-6748301	HepG2	liver:	n/a	chr7:6748054-6748068 chr7:6748055-6748063 chr7:6748052-6748070 chr7:6748054-6748069
9	FOXA2	chr7:6747930-6748292	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6681243..6682856-chr7:6746246..6748831,2	K562	blood:
2	chr7:6729955..6731866-chr7:6746781..6748682,2	MCF-7	breast:
3	chr7:6745463..6748475-chr7:6767656..6769994,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC073343.1-1	chr7:6748199-6748532	ENSG00000228010.1
2	lnc-AC073343.1-1	chr7:6746704-6748672	NONHSAT119061

Variant related genes	Relation type
ZNF12	TF binding region
PMS2CL	TF binding region
ENSG00000205903	Chromatin interaction
ENSG00000265245	Chromatin interaction
ENSG00000187953	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10244591	0.93[JPT][hapmap]
rs10272921	0.93[JPT][hapmap]
rs10951994	0.92[JPT][hapmap]
rs11770065	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11974158	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11979878	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11980762	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12531541	0.85[ASN][1000 genomes]
rs12537448	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs12673800	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs13224907	0.93[JPT][hapmap]
rs13247186	0.92[JPT][hapmap]
rs2140909	0.88[CHB][hapmap]
rs2881352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757482	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757483	0.93[ASN][1000 genomes]
rs3801033	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs3801038	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3801039	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs60514449	0.88[ASN][1000 genomes]
rs62439702	0.88[ASN][1000 genomes]
rs62439703	0.82[ASN][1000 genomes]
rs62439704	0.82[ASN][1000 genomes]
rs62439719	0.82[ASN][1000 genomes]
rs62439720	0.81[ASN][1000 genomes]
rs6463576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6463578	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6463580	0.93[JPT][hapmap]
rs6943677	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6944332	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6948965	0.91[AMR][1000 genomes]
rs6950197	1.00[CEU][hapmap]
rs6952131	0.87[ASN][1000 genomes]
rs6953825	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6954172	0.92[JPT][hapmap]
rs6954305	0.82[EUR][1000 genomes]
rs6958648	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6967414	0.93[ASN][1000 genomes]
rs6968879	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6969066	0.93[ASN][1000 genomes]
rs6971324	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6971621	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6971979	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6972017	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6974325	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6975002	0.82[ASN][1000 genomes]
rs6979127	0.88[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs6979158	0.82[ASN][1000 genomes]
rs7779296	0.92[JPT][hapmap]
rs7782227	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7786706	0.92[ASN][1000 genomes]
rs7786880	0.80[AMR][1000 genomes]
rs7798471	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7799134	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7804259	1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9639027	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv887439	chr7:6736332-6791749	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1015646	chr7:6738483-6779270	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv887440	chr7:6743097-6820508	Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv887441	chr7:6744957-6919214	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv1819001	chr7:6746810-6785602	Weak transcription Enhancers Flanking Active TSS Active TSS 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	12 gene(s)	inside rSNPs	diseases
8	nsv8039	chr7:6748111-6764886	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6747000-6768600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:6747200-6748800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:6747200-6749600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:6747400-6750600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:6747400-6752600	Weak transcription	HSMMtube	muscle
6	chr7:6747400-6757400	Weak transcription	Fetal Brain Female	brain
7	chr7:6748000-6749800	Active TSS	Liver	Liver
8	chr7:6748200-6749600	Enhancers	HepG2	liver

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