Variant report

Variant	rs17164923
Chromosome Location	chr5:126798031-126798032
allele	A/G
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	chr5:126798030-126798067	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000249577	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10491250	1.00[CEU][hapmap]
rs10519935	1.00[CEU][hapmap]
rs11241930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11747639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950754	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12109001	1.00[CEU][hapmap]
rs1363386	1.00[CEU][hapmap]
rs1529468	1.00[CEU][hapmap]
rs1587628	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1592960	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17164854	1.00[CEU][hapmap]
rs17164922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17164951	1.00[CEU][hapmap]
rs17164957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17165013	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs17165018	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs17165019	1.00[CEU][hapmap]
rs17684644	1.00[CEU][hapmap]
rs17684655	1.00[CEU][hapmap]
rs17684679	1.00[CEU][hapmap]
rs17684691	1.00[CEU][hapmap]
rs17684740	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs17684775	1.00[CEU][hapmap]
rs17685202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17763126	1.00[CEU][hapmap]
rs17763172	1.00[CEU][hapmap]
rs1990954	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs1990955	1.00[CEU][hapmap]
rs2042942	1.00[CEU][hapmap]
rs2134252	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2270933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851468	1.00[CEU][hapmap]
rs41298320	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55861432	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57626860	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6865700	1.00[CEU][hapmap]
rs6866275	1.00[CEU][hapmap]
rs6873921	1.00[CEU][hapmap]
rs6874260	1.00[CEU][hapmap]
rs6877383	1.00[CEU][hapmap]
rs6883445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6897163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73331215	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7737871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs929781	1.00[CEU][hapmap]
rs929782	1.00[CEU][hapmap]

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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126774600-126798800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:126789800-126830400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:126793400-126799600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:126793400-126805200	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:126795600-126799400	Weak transcription	HSMMtube	muscle
6	chr5:126797600-126805400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:126798000-126798200	Enhancers	Brain Inferior Temporal Lobe	brain

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