Variant report

Variant	rs12109166
Chromosome Location	chr5:90139386-90139387
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	RUNX3	chr5:90139208-90139696	GM12878	blood:	n/a	n/a
2	NFIC	chr5:90139255-90139615	GM12878	blood:	n/a	n/a
3	BATF	chr5:90139293-90139576	GM12878	blood:	n/a	chr5:90139462-90139473
4	MAX	chr5:90139357-90139693	NB4	blood:	n/a	n/a
5	BHLHE40	chr5:90139361-90139665	GM12878	blood:	n/a	n/a
6	MYC	chr5:90139348-90139631	NB4	blood:	n/a	n/a
7	NFIC	chr5:90139219-90139570	GM12878	blood:	n/a	n/a
8	BATF	chr5:90139290-90139599	GM12878	blood:	n/a	chr5:90139462-90139473
9	RUNX3	chr5:90139263-90139714	GM12878	blood:	n/a	n/a
10	BCLAF1	chr5:90139329-90139633	GM12878	blood:	n/a	n/a
11	CEBPB	chr5:90139150-90139390	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
GPR98	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11959536	1.00[EUR][1000 genomes]
rs2438336	1.00[EUR][1000 genomes]
rs2438341	1.00[EUR][1000 genomes]
rs2438346	1.00[EUR][1000 genomes]
rs4916693	1.00[EUR][1000 genomes]
rs6878024	1.00[EUR][1000 genomes]
rs73179344	1.00[EUR][1000 genomes]
rs7738012	1.00[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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90103000-90140800	Weak transcription	Brain Germinal Matrix	brain
2	chr5:90104600-90142000	Weak transcription	Brain Anterior Caudate	brain
3	chr5:90110200-90149600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:90112000-90151200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:90112000-90160600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:90112000-90175800	Weak transcription	Fetal Brain Female	brain
7	chr5:90112200-90142200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:90119200-90140800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:90127200-90144600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:90137000-90145400	Weak transcription	K562	blood
11	chr5:90137200-90144600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:90137400-90148800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:90137600-90144600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:90138000-90144400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:90138000-90146000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:90138000-90148600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:90138200-90142000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:90138800-90139400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:90138800-90140000	Enhancers	Primary hematopoietic stem cells	blood
20	chr5:90138800-90142200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:90139200-90139600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr5:90139200-90139600	Active TSS	Primary T killer memory cells from peripheral blood	blood

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