Variant report

Variant	rs4658042
Chromosome Location	chr1:196554402-196554403
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	TCF12	chr1:196553610-196554428	A549	lung:	n/a	n/a

Variant related genes	Relation type
MIR4735	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10737671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10737676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737678	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754193	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs10754194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754197	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10801536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10922081	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs10922087	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133987	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339947	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1339949	0.86[EUR][1000 genomes]
rs1339951	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1360143	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416960	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416966	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1416970	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1416971	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1538683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556961	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1571489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16839848	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16839856	1.00[JPT][hapmap]
rs16839872	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16839878	1.00[JPT][hapmap]
rs16839881	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16839884	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16839886	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs16839905	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs16839906	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs16839910	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16839919	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16840397	1.00[JPT][hapmap]
rs2335906	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs2335907	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4294368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4314834	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs4316314	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4405100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515738	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs4518841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4562566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4601531	0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614205	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625226	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs4633231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658040	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs4658043	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479718	1.00[JPT][hapmap]
rs6663649	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs6670223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675592	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680722	0.86[EUR][1000 genomes]
rs6680890	0.88[AFR][1000 genomes]
rs6688468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702610	0.82[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7531491	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7533533	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs7540922	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs7541165	0.82[EUR][1000 genomes]
rs7544266	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7544383	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7552170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1009233	chr1:196301712-196568874	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
3	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196527800-196559400	Weak transcription	Ovary	ovary
2	chr1:196547800-196556200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:196547800-196559000	Weak transcription	Liver	Liver
4	chr1:196548200-196557400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:196548400-196557600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:196554400-196555000	Enhancers	A549	lung

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