Variant report

Variant	rs1609894
Chromosome Location	chr12:41166046-41166047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10735959	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10748155	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10748156	0.84[AFR][1000 genomes]
rs10784861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12368044	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1579799	0.85[AMR][1000 genomes]
rs1579800	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1584098	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1596524	0.85[AMR][1000 genomes]
rs1596530	0.83[AMR][1000 genomes]
rs1947050	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4767990	0.85[AMR][1000 genomes]
rs4768308	0.91[AFR][1000 genomes]
rs4768310	0.83[AMR][1000 genomes]
rs6581946	1.00[AMR][1000 genomes]
rs6581956	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6581960	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6581961	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6581962	0.85[AFR][1000 genomes]
rs6581963	0.85[AFR][1000 genomes]
rs7132626	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7133020	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7294835	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7295663	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7298569	0.85[AMR][1000 genomes]
rs7302071	0.83[AMR][1000 genomes]
rs7312640	0.85[AMR][1000 genomes]
rs7315033	0.89[AFR][1000 genomes]
rs7960628	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7978716	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832379	chr12:41054440-41232749	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2751098	chr12:41082399-41180235	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1044513	chr12:41091822-41175151	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv558696	chr12:41092666-41172010	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv832380	chr12:41132306-41323961	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv469362	chr12:41155000-41206520	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv558697	chr12:41155000-41206520	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv469363	chr12:41155000-41214848	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv558698	chr12:41155000-41214848	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41146200-41187400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:41164000-41166600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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