Variant report

Variant	rs12936954
Chromosome Location	chr17:33802950-33802951
allele	A/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	chr17:33802909-33803842	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000267349	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12451876	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12936256	0.84[EUR][1000 genomes]
rs12937961	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12939675	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12949245	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12953115	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2304967	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34121367	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34620580	0.84[EUR][1000 genomes]
rs34646901	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34656640	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34734788	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34747751	0.85[EUR][1000 genomes]
rs35057074	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35367381	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35563348	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3744372	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55668225	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56033496	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56061417	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67338337	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72825999	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72826000	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8064887	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8065289	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8066132	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8079653	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8082478	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574741	chr17:33552275-33827134	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1056116	chr17:33691457-33815452	Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33796000-33803000	Weak transcription	Fetal Thymus	thymus
2	chr17:33800400-33807200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr17:33800400-33809400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:33800600-33803200	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr17:33800800-33803600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:33800800-33804200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
7	chr17:33800800-33807200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr17:33801000-33803400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr17:33801000-33804400	ZNF genes & repeats	Primary T cells from cord blood	blood
10	chr17:33801000-33805200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr17:33801200-33804000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:33801200-33804200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr17:33801200-33804200	Strong transcription	Dnd41	blood
14	chr17:33801800-33809400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr17:33802000-33803400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
16	chr17:33802600-33803800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:33802600-33804600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr17:33802600-33806200	Weak transcription	GM12878-XiMat	blood

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