Variant report

Variant	rs3896232
Chromosome Location	chr1:45009801-45009802
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	ZNF263	chr1:45009515-45009836	HEK293-T-REx	kidney:	n/a	n/a
2	BACH1	chr1:45008944-45009845	H1-hESC	embryonic stem cell:	n/a	n/a
3	HDAC2	chr1:45008756-45009843	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr1:45008602-45009819	H1-hESC	embryonic stem cell:	n/a	chr1:45008992-45009010
5	MXI1	chr1:45008880-45009809	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr1:45008019-45009840	H1-hESC	embryonic stem cell:	n/a	chr1:45008952-45008971 chr1:45008993-45009003 chr1:45008697-45008711 chr1:45008234-45008244
7	JUND	chr1:45008375-45009834	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTBP2	chr1:45008341-45010113	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:44999769..45001806-chr1:45008456..45010652,2	K562	blood:

Variant related genes	Relation type
MIR5584	TF binding region

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11577681	0.83[CEU][hapmap]
rs12065045	0.97[GIH][hapmap]
rs12403454	0.83[CEU][hapmap];0.92[GIH][hapmap]
rs72895588	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72895590	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs746733	0.83[CEU][hapmap];0.86[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:44998800-45017800	Weak transcription	Right Atrium	heart
2	chr1:44998800-45022000	Weak transcription	HepG2	liver
3	chr1:45004800-45015200	Enhancers	Brain Substantia Nigra	brain
4	chr1:45007200-45015800	Enhancers	Brain Angular Gyrus	brain
5	chr1:45007600-45010400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:45007600-45011600	Enhancers	Brain Anterior Caudate	brain
7	chr1:45007600-45016600	Enhancers	Brain Cingulate Gyrus	brain
8	chr1:45007600-45016600	Enhancers	Brain Hippocampus Middle	brain
9	chr1:45008000-45016400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr1:45008200-45010000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:45008200-45012800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:45008600-45010000	Enhancers	Primary hematopoietic stem cells	blood
13	chr1:45008600-45010000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:45008800-45010000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:45008800-45012800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:45009200-45010000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:45009200-45012800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:45009400-45010000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:45009400-45010200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
20	chr1:45009600-45010000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:45009600-45010000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
22	chr1:45009600-45010000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:45009600-45010000	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr1:45009600-45010200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:45009600-45010200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:45009600-45011400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
27	chr1:45009600-45012000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
28	chr1:45009600-45012400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:45009600-45021200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:45009800-45010800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
31	chr1:45009800-45012000	Enhancers	H9 Cell Line	embryonic stem cell
32	chr1:45009800-45012000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
33	chr1:45009800-45012800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

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