Variant report

Variant	rs12990843
Chromosome Location	chr2:53108688-53108689
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	FOXA1	chr2:53108628-53109134	A549	lung:	n/a	n/a
2	FOSL2	chr2:53108679-53109166	A549	lung:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
3	TCF12	chr2:53108681-53109251	A549	lung:	n/a	n/a
4	FOSL1	chr2:53108676-53109299	HCT-116	colon:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
5	CBX3	chr2:53108658-53109304	HCT-116	colon:	n/a	n/a
6	SIN3AK20	chr2:53108619-53109262	MCF-7	breast:	n/a	n/a
7	SP1	chr2:53108628-53109273	A549	lung:	n/a	n/a
8	SP1	chr2:53108669-53109332	HCT-116	colon:	n/a	n/a
9	RCOR1	chr2:53108549-53109377	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53103066..53106486-chr2:53106611..53109718,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232668	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10164801	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10164868	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10167421	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10168840	0.91[EUR][1000 genomes]
rs10173886	0.94[EUR][1000 genomes]
rs10179810	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10184255	0.85[EUR][1000 genomes]
rs10191273	0.93[EUR][1000 genomes]
rs10203699	0.93[EUR][1000 genomes]
rs10206560	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10208858	0.94[EUR][1000 genomes]
rs10865272	0.95[EUR][1000 genomes]
rs11888200	0.80[EUR][1000 genomes]
rs12475542	0.96[EUR][1000 genomes]
rs12477231	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12611901	0.81[ASN][1000 genomes]
rs12614959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12617374	0.96[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs12617738	0.95[EUR][1000 genomes]
rs12618983	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12713227	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs12713228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12713229	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs12713230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12713231	0.92[EUR][1000 genomes]
rs12713232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713233	0.97[EUR][1000 genomes]
rs13002328	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13003962	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13014502	0.81[ASN][1000 genomes]
rs13030509	0.96[EUR][1000 genomes]
rs13387682	0.96[CEU][hapmap];0.90[YRI][hapmap]
rs1376563	0.93[EUR][1000 genomes]
rs1376567	0.95[EUR][1000 genomes]
rs1376569	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1376570	0.92[CEU][hapmap];0.84[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs1451455	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1451456	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1451458	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1451460	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1597653	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17504530	0.92[EUR][1000 genomes]
rs1828337	0.90[EUR][1000 genomes]
rs1828338	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1839770	0.96[EUR][1000 genomes]
rs1839771	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864534	0.96[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs2356675	0.86[ASN][1000 genomes]
rs2356680	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2356681	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36130286	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4143203	0.86[EUR][1000 genomes]
rs4525730	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545310	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715847	0.93[EUR][1000 genomes]
rs6715857	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6725912	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6737483	0.85[EUR][1000 genomes]
rs6746666	0.92[CEU][hapmap];0.90[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs6754205	0.96[EUR][1000 genomes]
rs6754423	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67939368	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs724859	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs724860	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74181216	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7577692	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998380	chr2:52891706-53222155	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	esv2763631	chr2:52910862-53169629	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006244	chr2:52958322-53169617	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1005813	chr2:52959769-53114865	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1010978	chr2:52959769-53249951	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1014068	chr2:52960353-53169617	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv520722	chr2:53039770-53421015	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1010237	chr2:53072736-53116413	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	nsv581978	chr2:53091691-53227749	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	nsv874136	chr2:53101066-53218774	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
11	esv3358006	chr2:53108148-53112546	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53105600-53121800	Weak transcription	Pancreas	Pancrea
2	chr2:53107200-53109000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:53107600-53109000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:53107800-53109000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:53107800-53109200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:53108200-53109200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:53108200-53119800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:53108400-53108800	Weak transcription	A549	lung
9	chr2:53108600-53109400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:53108600-53109400	Enhancers	Hela-S3	cervix

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