Variant report

Variant	rs7964896
Chromosome Location	chr12:57982794-57982795
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	USF1	chr12:57982685-57983032	K562	blood:	n/a	chr12:57982905-57982916
2	USF1	chr12:57982784-57983019	K562	blood:	n/a	chr12:57982905-57982916

No.	Distal block	Cell Line	Cell type
1	chr12:57867428..57869437-chr12:57981314..57983713,2	MCF-7	breast:
2	chr12:57980950..57983241-chr12:58144610..58146374,2	K562	blood:
3	chr12:57912977..57915382-chr12:57982264..57984684,2	MCF-7	breast:
4	chr12:57980232..57983207-chr12:58117360..58119823,3	MCF-7	breast:

Variant related genes	Relation type
PIP4K2C	TF binding region
ENSG00000166987	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000175197	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10747780	0.91[ASN][1000 genomes]
rs11172262	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1806652	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2619439	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34181394	0.81[EUR][1000 genomes]
rs60586224	0.83[EUR][1000 genomes]
rs71461330	0.86[EUR][1000 genomes]
rs7305391	0.85[EUR][1000 genomes]
rs7314872	0.85[EUR][1000 genomes]
rs812315	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8873	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
6	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv725	chr12:57966549-57993808	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	n/a
10	nsv53146	chr12:57982442-57983701	Weak transcription Enhancers	TF binding region Chromatin interactive region	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7964896	AC025165.8	cis	Nerve Tibial	GTEx
rs7964896	ARHGEF25	cis	Nerve Tibial	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57964400-57984400	Weak transcription	Pancreas	Pancrea
2	chr12:57966400-57984000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:57966600-57984000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:57966600-57984600	Weak transcription	Gastric	stomach
5	chr12:57966800-57984400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:57970600-57984200	Weak transcription	Fetal Brain Male	brain
7	chr12:57972200-57984200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:57972200-57984400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:57975600-57984200	Weak transcription	Brain Substantia Nigra	brain
10	chr12:57975800-57984200	Weak transcription	Brain Angular Gyrus	brain
11	chr12:57975800-57984400	Weak transcription	Aorta	Aorta
12	chr12:57976200-57984200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:57976400-57984400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:57976600-57984200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:57976800-57984200	Weak transcription	Brain Anterior Caudate	brain
16	chr12:57977000-57984200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:57977000-57984400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:57977200-57984200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:57977600-57984200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:57977800-57984200	Weak transcription	HepG2	liver
21	chr12:57978600-57982800	Weak transcription	K562	blood
22	chr12:57978800-57984200	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:57979800-57984200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:57980400-57984200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:57980600-57984200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:57980600-57984200	Weak transcription	Brain Germinal Matrix	brain
27	chr12:57980800-57984200	Weak transcription	Fetal Brain Female	brain
28	chr12:57981000-57984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:57982200-57984400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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