Variant report

Variant	rs16840139
Chromosome Location	chr1:158392324-158392325
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	chr1:158391983-158392426	H1-hESC	embryonic stem cell:	n/a	n/a
2	GATA3	chr1:158391991-158392534	MCF-7	breast:	n/a	chr1:158392495-158392502 chr1:158392376-158392385
3	SP1	chr1:158392102-158392357	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr1:158391949-158392390	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr1:158392074-158392326	H1-hESC	embryonic stem cell:	n/a	n/a
6	TEAD4	chr1:158391958-158392422	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
OR10K2	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1418840	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16840136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16840141	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16840143	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16840182	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16840184	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2023633	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2213945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2220631	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2860016	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28866916	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55702828	1.00[AMR][1000 genomes]
rs56773217	1.00[AMR][1000 genomes]
rs58592764	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59604063	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60150627	1.00[AMR][1000 genomes]
rs6684251	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6691971	1.00[AMR][1000 genomes]
rs73012005	1.00[AMR][1000 genomes]
rs73013915	1.00[AMR][1000 genomes]
rs73013919	1.00[AMR][1000 genomes]
rs73013923	1.00[AMR][1000 genomes]
rs73013934	1.00[AMR][1000 genomes]
rs73013940	1.00[AMR][1000 genomes]
rs73015825	1.00[AMR][1000 genomes]
rs73017709	1.00[AMR][1000 genomes]
rs73017717	1.00[AMR][1000 genomes]
rs73017739	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73019705	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73019756	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73021774	0.96[AFR][1000 genomes]
rs73021906	1.00[AMR][1000 genomes]
rs73021929	1.00[AMR][1000 genomes]
rs73023804	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73023822	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73023829	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73023942	1.00[AMR][1000 genomes]
rs73023945	1.00[AMR][1000 genomes]
rs73023947	1.00[AMR][1000 genomes]
rs73025843	1.00[AMR][1000 genomes]
rs73027731	1.00[AMR][1000 genomes]
rs73027744	1.00[AMR][1000 genomes]
rs74121843	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74121844	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74121858	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7532088	1.00[AMR][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	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv872480	chr1:158153526-158450238	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv998569	chr1:158317392-158443389	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158391400-158393000	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr1:158391400-158393000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:158391600-158392600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr1:158391600-158392600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:158391600-158393600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:158391800-158393000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr1:158392000-158392400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:158392200-158392400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr1:158392200-158392600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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