Variant report

Variant	rs252727
Chromosome Location	chr16:46751452-46751453
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46722609..46724172-chr16:46751390..46753908,2	MCF-7	breast:
2	chr16:46741908..46744593-chr16:46750303..46752897,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091651	Chromatin interaction
ENSG00000069329	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10902629	1.00[AMR][1000 genomes]
rs11860636	1.00[ASW][hapmap];1.00[LWK][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12598707	1.00[AMR][1000 genomes]
rs1436435	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1466170	1.00[AMR][1000 genomes]
rs1530895	1.00[AMR][1000 genomes]
rs153259	0.85[AFR][1000 genomes]
rs1542292	1.00[AMR][1000 genomes]
rs1641120	1.00[AMR][1000 genomes]
rs1645939	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1651658	1.00[AMR][1000 genomes]
rs1651659	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs166096	1.00[AMR][1000 genomes]
rs168745	1.00[AMR][1000 genomes]
rs1698957	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs185213	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1865837	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1865838	1.00[AMR][1000 genomes]
rs194054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs194055	1.00[AMR][1000 genomes]
rs1992075	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1992078	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2033673	1.00[AMR][1000 genomes]
rs2034599	1.00[AMR][1000 genomes]
rs2334116	1.00[YRI][hapmap]
rs250420	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs250421	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs252723	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs252724	1.00[AMR][1000 genomes]
rs252725	1.00[AMR][1000 genomes]
rs252728	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs252732	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs252733	1.00[AMR][1000 genomes]
rs252734	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36309	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36311	1.00[AMR][1000 genomes]
rs36313	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36314	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36317	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36460	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs36461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36463	1.00[AMR][1000 genomes]
rs36465	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36466	1.00[LWK][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36467	1.00[AMR][1000 genomes]
rs36470	1.00[LWK][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36473	1.00[AMR][1000 genomes]
rs36474	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36475	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36477	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36480	1.00[YRI][hapmap]
rs36482	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs396907	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs40164	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs408906	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41232	1.00[AMR][1000 genomes]
rs414928	1.00[AMR][1000 genomes]
rs420560	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs425556	1.00[AMR][1000 genomes]
rs438275	1.00[AMR][1000 genomes]
rs449778	1.00[AMR][1000 genomes]
rs4966488	1.00[YRI][hapmap]
rs4966571	1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4966603	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4967248	0.83[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4967259	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4967594	1.00[AMR][1000 genomes]
rs4967595	1.00[AMR][1000 genomes]
rs62057622	1.00[AMR][1000 genomes]
rs633699	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs637583	1.00[AMR][1000 genomes]
rs6598632	1.00[TSI][hapmap]
rs6598661	1.00[AMR][1000 genomes]
rs6598679	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6598781	1.00[AMR][1000 genomes]
rs695997	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs698417	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs698419	1.00[AMR][1000 genomes]
rs700580	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs700581	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7184436	1.00[AMR][1000 genomes]
rs7192389	1.00[AMR][1000 genomes]
rs7198683	1.00[AMR][1000 genomes]
rs7206393	1.00[AMR][1000 genomes]
rs794283	1.00[AMR][1000 genomes]
rs794557	1.00[AMR][1000 genomes]
rs794558	1.00[AMR][1000 genomes]
rs794559	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs797016	1.00[AMR][1000 genomes]
rs8044120	1.00[AMR][1000 genomes]
rs8046818	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8047302	1.00[AMR][1000 genomes]
rs8048535	1.00[AMR][1000 genomes]
rs8049734	1.00[AMR][1000 genomes]
rs8059285	1.00[AMR][1000 genomes]
rs808078	1.00[YRI][hapmap]
rs808428	1.00[AMR][1000 genomes]
rs808436	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs811196	0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs811267	1.00[AMR][1000 genomes]
rs811734	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs937659	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9922581	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9924386	1.00[AMR][1000 genomes]
rs9925083	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9935045	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799780	chr16:46386457-46875496	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1060734	chr16:46463770-46768102	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1064289	chr16:46463770-46801977	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
5	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
6	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
10	nsv916976	chr16:46505597-46801868	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv526656	chr16:46539392-46846663	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	esv1792701	chr16:46709686-46751452	Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1059598	chr16:46721805-46762219	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv542913	chr16:46721805-46762219	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
15	nsv1064272	chr16:46721805-46768134	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv542914	chr16:46721805-46768134	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	nsv1067038	chr16:46721805-46797514	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
18	nsv1066472	chr16:46721805-46801769	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
19	nsv1065253	chr16:46721805-46824369	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer 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	31 gene(s)	inside rSNPs	diseases
20	nsv1059049	chr16:46721805-46859239	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
21	nsv1061651	chr16:46721805-46915511	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
22	nsv1060982	chr16:46721805-46938858	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46725600-46752200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr16:46731200-46755800	Weak transcription	Fetal Muscle Leg	muscle
3	chr16:46745800-46752000	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr16:46746800-46769600	Weak transcription	Spleen	Spleen
5	chr16:46748800-46753400	Weak transcription	Right Atrium	heart
6	chr16:46749000-46751800	Weak transcription	Fetal Heart	heart
7	chr16:46750200-46753200	Weak transcription	Psoas Muscle	Psoas
8	chr16:46750600-46752600	Genic enhancers	Left Ventricle	heart
9	chr16:46750600-46752600	Genic enhancers	Right Ventricle	heart
10	chr16:46750600-46753400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:46751000-46752000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr16:46751000-46752400	Enhancers	Fetal Brain Female	brain
13	chr16:46751200-46751600	Enhancers	Fetal Brain Male	brain
14	chr16:46751400-46752000	Genic enhancers	Skeletal Muscle Male	skeletal muscle

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