Variant report

Variant	rs12698946
Chromosome Location	chr7:70301346-70301347
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	SRF	chr7:70301321-70301670	H1-hESC	embryonic stem cell:	n/a	chr7:70301484-70301502
2	SRF	chr7:70301255-70301686	H1-hESC	embryonic stem cell:	n/a	chr7:70301484-70301502
3	POLR2A	chr7:70301314-70301565	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000236978	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10226378	0.93[EUR][1000 genomes]
rs10244947	0.94[EUR][1000 genomes]
rs10245302	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10248357	0.94[EUR][1000 genomes]
rs10252997	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10258059	0.94[EUR][1000 genomes]
rs10258179	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10259518	0.93[EUR][1000 genomes]
rs10263077	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1105549	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11486733	0.93[EUR][1000 genomes]
rs12698945	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12698948	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12698951	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12698952	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12698953	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12698954	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12698955	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13232813	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13233533	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13240442	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13240454	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13240507	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13243605	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13438596	0.93[EUR][1000 genomes]
rs1881013	0.86[EUR][1000 genomes]
rs28499173	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28545657	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28559780	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28610179	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28638367	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28796386	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28878291	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34156143	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34346022	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34382948	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34440019	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34502147	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34752673	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34843773	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35716818	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35725834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35872831	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35926007	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35945582	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55785505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55922222	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55976841	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56148881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56191526	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56356827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56376908	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56402150	0.93[EUR][1000 genomes]
rs56403077	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6460565	0.93[EUR][1000 genomes]
rs6460566	0.93[EUR][1000 genomes]
rs6460567	0.93[EUR][1000 genomes]
rs6460568	0.93[EUR][1000 genomes]
rs66970908	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs67936649	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6946406	0.85[ASN][1000 genomes]
rs6953195	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6962634	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7786779	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025164	chr7:70061655-70469358	Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Weak transcription 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	2 gene(s)	inside rSNPs	diseases
2	nsv538931	chr7:70061655-70469358	Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1017876	chr7:70073764-70434599	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1028853	chr7:70211620-70523331	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv533212	chr7:70220687-70511129	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv888341	chr7:70249358-70316365	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised 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
8	nsv429772	chr7:70250125-70357061	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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
9	nsv607437	chr7:70251651-70568354	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1031764	chr7:70271645-70420426	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1034662	chr7:70275712-70722953	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1034508	chr7:70277984-70420426	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1019598	chr7:70285963-70358327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv429773	chr7:70285994-70357061	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv3350369	chr7:70288094-70503884	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv429774	chr7:70294296-70357061	ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv428503	chr7:70295677-70463201	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv1016072	chr7:70297559-70358327	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1030514	chr7:70300719-70592796	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv1026024	chr7:70301346-70594292	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12698946	WBSCR17	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70295400-70301800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:70301200-70312200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:70301200-70314200	Weak transcription	H1 Cell Line	embryonic stem cell

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