Variant report

Variant	rs408516
Chromosome Location	chr21:46017607-46017608
allele	C/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	MAX	chr21:46017598-46018390	H1-hESC	embryonic stem cell:	n/a	n/a
2	SETDB1	chr21:46017565-46019237	U2OS	brain:	n/a	n/a
3	MAX	chr21:46017549-46017853	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
KRTAP10-7	TF binding region
ENSG00000256212	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs116344	0.82[EUR][1000 genomes]
rs1211088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211089	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211103	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1211118	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1211121	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1211122	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1211123	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1211129	0.84[EUR][1000 genomes]
rs1211130	0.84[EUR][1000 genomes]
rs12627104	0.93[ASN][1000 genomes]
rs12627414	0.88[ASN][1000 genomes]
rs233298	0.87[ASN][1000 genomes]
rs233299	0.87[ASN][1000 genomes]
rs233300	0.91[ASN][1000 genomes]
rs366534	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs369720	0.84[ASN][1000 genomes]
rs370092	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs377234	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs377573	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs382935	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs384645	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs385033	0.93[ASN][1000 genomes]
rs389936	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390630	0.95[EUR][1000 genomes]
rs392451	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs392686	0.85[EUR][1000 genomes]
rs395781	0.84[EUR][1000 genomes]
rs398680	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs400170	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs400406	0.95[EUR][1000 genomes]
rs403981	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs404341	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs408183	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs408285	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs408958	0.84[EUR][1000 genomes]
rs409239	0.84[EUR][1000 genomes]
rs409893	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415753	0.85[EUR][1000 genomes]
rs416056	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs417538	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs418260	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs425276	0.84[EUR][1000 genomes]
rs437149	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs437371	0.84[EUR][1000 genomes]
rs438444	0.95[EUR][1000 genomes]
rs442110	0.86[ASN][1000 genomes]
rs442226	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs442761	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs442849	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443484	0.95[EUR][1000 genomes]
rs446817	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs447568	0.83[ASN][1000 genomes]
rs452002	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs452547	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs455906	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs459644	0.95[EUR][1000 genomes]
rs463876	0.92[EUR][1000 genomes]
rs466628	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56274513	0.89[ASN][1000 genomes]
rs58029281	0.81[ASN][1000 genomes]
rs58757665	0.97[ASN][1000 genomes]
rs659638	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913943	chr21:45740823-46031810	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv913946	chr21:45838632-46031810	Bivalent Enhancer ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv913948	chr21:45860912-46031810	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv1056424	chr21:45894901-46031810	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544475	chr21:45894901-46031810	Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1055163	chr21:45895663-46031810	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1065798	chr21:45941000-46097463	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv869108	chr21:45941000-46097463	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv544476	chr21:45941000-46097463	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv913950	chr21:45985068-46097463	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv913952	chr21:45988426-46031810	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	esv2751931	chr21:45990446-46031810	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv587810	chr21:45992131-46031810	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
16	nsv913953	chr21:46012524-46031810	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 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	chr21:46002400-46018200	Weak transcription	Right Atrium	heart
2	chr21:46014000-46018000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr21:46014200-46017800	Weak transcription	NHEK	skin
4	chr21:46014200-46018200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr21:46014200-46021400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr21:46014600-46021600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr21:46016400-46017800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:46016600-46021200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr21:46016800-46017800	Weak transcription	HMEC	breast
10	chr21:46017600-46018200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr21:46017600-46018600	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr21:46017600-46018600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr21:46017600-46018800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr21:46017600-46018800	Enhancers	HUES64 Cell Line	embryonic stem cell

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