Variant report

Variant	rs12097239
Chromosome Location	chr1:227912474-227912475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227910908-227920562	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:227910941-227920625	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:227911546-227912860	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227912232..227914345-chr1:228021397..228023530,2	K562	blood:
2	chr1:227899761..227902158-chr1:227912369..227914847,2	K562	blood:
3	chr1:227907636..227909254-chr1:227910705..227913519,2	K562	blood:
4	chr1:227906153..227908527-chr1:227912474..227914252,2	K562	blood:
5	chr1:227885139..227888079-chr1:227910655..227913000,2	K562	blood:

No data

Variant related genes	Relation type
SNAP47	TF binding region
ENSG00000215812	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10799444	0.83[YRI][hapmap];0.95[AFR][1000 genomes]
rs10799445	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916166	0.83[YRI][hapmap]
rs10916167	0.86[ASW][hapmap];0.87[MKK][hapmap];0.84[YRI][hapmap]
rs10916180	0.86[ASW][hapmap];0.88[MKK][hapmap];0.88[YRI][hapmap]
rs10916204	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11576992	0.97[AFR][1000 genomes]
rs11581704	0.87[YRI][hapmap]
rs12073225	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12077397	0.95[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119889	0.87[YRI][hapmap]
rs12120182	0.88[YRI][hapmap]
rs12123996	0.81[ASW][hapmap]
rs12127819	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12132761	0.82[AFR][1000 genomes]
rs12138198	0.96[AFR][1000 genomes]
rs12138229	0.97[AFR][1000 genomes]
rs12141801	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1995019	0.84[YRI][hapmap]
rs3088389	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656661	0.81[MKK][hapmap]
rs6659349	0.88[YRI][hapmap]
rs6664307	0.80[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6672530	0.86[ASW][hapmap];0.84[YRI][hapmap]
rs6691443	0.93[ASW][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap]
rs6696239	0.86[ASW][hapmap];0.85[MKK][hapmap]
rs7538206	0.89[AFR][1000 genomes]
rs7540382	0.91[AFR][1000 genomes]
rs7549475	0.93[ASW][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap]
rs9726691	0.86[ASW][hapmap];0.83[YRI][hapmap]

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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv945344	chr1:227899939-227917776	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
8	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12097239	JMJD4	cis	multi-tissue	Pritchard
rs12097239	TAF5L	cis	parietal	SCAN
rs12097239	WDR26	cis	cerebellum	SCAN
rs12097239	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs12097239	ZNF678	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227911400-227915600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:227911800-227912600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:227912200-227913400	Enhancers	Fetal Muscle Leg	muscle

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