Variant report

Variant	rs2650940
Chromosome Location	chr5:17352798-17352799
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	EP300	chr5:17352504-17352852	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr5:17351965-17353092	H1-neurons	neurons:	n/a	n/a
3	REST	chr5:17352185-17352943	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:17348620..17350126-chr5:17350951..17353449,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248223	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10074496	0.82[EUR][1000 genomes]
rs10462609	0.82[EUR][1000 genomes]
rs11950287	0.83[EUR][1000 genomes]
rs13355635	0.82[EUR][1000 genomes]
rs182441	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1827400	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2134241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454946	0.84[EUR][1000 genomes]
rs2650923	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650935	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2650936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650937	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650938	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650939	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650943	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652638	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2652639	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2652641	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2652643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652646	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652647	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652648	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28476505	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs298530	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs298531	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs298532	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs298534	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs298535	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs298536	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs298546	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs298547	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs298548	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs298550	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs298558	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298559	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298560	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298562	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs299384	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs299385	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs299386	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56663279	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56705013	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58062922	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58468495	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6862515	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73052871	0.82[EUR][1000 genomes]
rs73052881	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73052887	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73052888	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73052898	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73052901	0.83[EUR][1000 genomes]
rs73054809	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73054823	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7719794	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv461988	chr5:17296342-17484038	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv597313	chr5:17296342-17484038	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv830219	chr5:17325802-17518914	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv2763872	chr5:17342482-17358269	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
6	esv3432739	chr5:17342737-17357177	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
7	esv19164	chr5:17342748-17357008	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
8	esv1836524	chr5:17347702-17356239	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
9	nsv441940	chr5:17347702-17356239	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
10	nsv597314	chr5:17347706-17352859	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	nsv597315	chr5:17347706-17353314	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	nsv597316	chr5:17347706-17353999	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv597317	chr5:17347706-17354665	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
14	nsv597318	chr5:17347706-17356166	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
15	nsv597319	chr5:17347706-17356536	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
16	nsv597320	chr5:17347706-17356614	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
17	nsv514292	chr5:17348248-17355010	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
18	nsv597321	chr5:17351275-17352859	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
19	nsv597322	chr5:17351275-17353999	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	nsv597323	chr5:17351275-17356166	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
21	nsv597324	chr5:17352210-17356614	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
22	nsv597325	chr5:17352326-17356166	Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
23	nsv597326	chr5:17352326-17356614	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
24	nsv597327	chr5:17352407-17356166	Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
25	nsv597328	chr5:17352407-17356614	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
26	nsv597329	chr5:17352741-17356614	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr5:17344600-17358400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:17351000-17353000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr5:17351200-17353000	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr5:17351200-17353000	Enhancers	Fetal Brain Male	brain
5	chr5:17351400-17354400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:17352000-17352800	Enhancers	H9 Cell Line	embryonic stem cell
7	chr5:17352000-17353000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr5:17352400-17352800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:17352400-17353000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr5:17352600-17353000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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