Variant report

Variant	rs56369903
Chromosome Location	chr17:16838594-16838595
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	POLR2A	chr17:16838121-16838629	GM12892	blood:	n/a	n/a
2	POLR2A	chr17:16837722-16839628	GM15510	blood:	n/a	n/a
3	FOS	chr17:16838506-16838757	MCF10A-Er-Src	breast:	n/a	chr17:16838660-16838669 chr17:16838659-16838668
4	POLR2A	chr17:16836222-16840329	GM12891	blood:	n/a	n/a
5	POLR2A	chr17:16836887-16840387	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:16838115-16839574	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:16836764-16840269	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:16838016-16839751	GM12892	blood:	n/a	n/a
9	POLR2A	chr17:16837244-16839590	GM12892	blood:	n/a	n/a
10	POLR2A	chr17:16836787-16839697	GM18951	blood:	n/a	n/a
11	FOSL2	chr17:16838479-16838773	HepG2	liver:	n/a	chr17:16838660-16838669 chr17:16838659-16838668
12	POLR2A	chr17:16837386-16839567	GM19193	blood:	n/a	n/a
13	STAT5A	chr17:16838177-16839729	GM12878	blood:	n/a	n/a
14	MTA3	chr17:16837573-16840462	GM12878	blood:	n/a	n/a
15	POLR2A	chr17:16835967-16839770	GM12878	blood:	n/a	n/a
16	STAT5A	chr17:16837390-16842245	GM12878	blood:	n/a	n/a
17	POLR2A	chr17:16834953-16843440	GM12878	blood:	n/a	n/a
18	NFATC1	chr17:16837763-16839768	GM12878	blood:	n/a	n/a
19	POLR2A	chr17:16838019-16839544	GM12891	blood:	n/a	n/a
20	NFATC1	chr17:16838154-16839809	GM12878	blood:	n/a	n/a
21	FOS	chr17:16838564-16838699	MCF10A-Er-Src	breast:	n/a	chr17:16838660-16838669 chr17:16838659-16838668
22	POLR2A	chr17:16837443-16839551	GM12878	blood:	n/a	n/a
23	FOS	chr17:16838583-16838715	MCF10A-Er-Src	breast:	n/a	chr17:16838660-16838669 chr17:16838659-16838668
24	POLR2A	chr17:16837871-16839517	GM12892	blood:	n/a	n/a
25	POLR2A	chr17:16837194-16839652	GM18505	blood:	n/a	n/a

Variant related genes	Relation type
TBC1D27	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1004439	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10468462	0.81[ASN][1000 genomes]
rs11649835	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11650590	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11650981	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11651352	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12325872	0.94[ASN][1000 genomes]
rs35380019	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4343329	0.80[EUR][1000 genomes]
rs55635506	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55770108	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56035746	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56092540	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56396775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56408153	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62065417	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62065418	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62065421	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62065423	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62065424	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62065425	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62065426	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62065427	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62065430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7214221	0.94[ASN][1000 genomes]
rs7218682	0.94[ASN][1000 genomes]
rs73980239	0.94[ASN][1000 genomes]
rs73980240	0.94[ASN][1000 genomes]
rs73980241	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv2753951	chr17:16660721-16848750	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2755100	chr17:16660721-16848750	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv833379	chr17:16683585-16859539	Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1055688	chr17:16800788-16868860	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv907726	chr17:16821204-16875636	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56369903	LOC96597	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16834000-16841000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr17:16834800-16842800	Weak transcription	Spleen	Spleen
3	chr17:16836200-16840800	Weak transcription	GM12878-XiMat	blood
4	chr17:16837000-16842000	Weak transcription	Brain Anterior Caudate	brain
5	chr17:16837200-16844400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr17:16838400-16838600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
7	chr17:16838400-16838600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr17:16838400-16838800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr17:16838400-16839000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr17:16838400-16843000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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