Variant report

Variant	rs2183225
Chromosome Location	chr1:196578716-196578717
allele	G/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	GATA2	chr1:196577184-196578832	SH-SY5Y	brain:	n/a	chr1:196578008-196578021 chr1:196577813-196577824
2	MYC	chr1:196577578-196578815	H1-hESC	embryonic stem cell:	n/a	chr1:196577658-196577667 chr1:196578657-196578666 chr1:196578159-196578169
3	SETDB1	chr1:196578079-196578722	U2OS	brain:	n/a	n/a
4	ZNF143	chr1:196577284-196578739	H1-hESC	embryonic stem cell:	n/a	chr1:196577964-196577974
5	CEBPB	chr1:196578514-196578852	HepG2	liver:	n/a	chr1:196578654-196578665
6	SIN3A	chr1:196576883-196578976	H1-hESC	embryonic stem cell:	n/a	n/a
7	TBP	chr1:196577168-196578784	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:196576870-196579084	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:196577186-196578788	H1-hESC	embryonic stem cell:	n/a	n/a
10	CHD1	chr1:196576411-196579113	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr1:196577156-196578831	H1-hESC	embryonic stem cell:	n/a	chr1:196578044-196578052 chr1:196578654-196578665
12	USF2	chr1:196577847-196578765	H1-hESC	embryonic stem cell:	n/a	n/a
13	CEBPB	chr1:196578456-196579000	IMR90	lung:	n/a	chr1:196578654-196578665
14	CHD2	chr1:196577189-196578907	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr1:196577465-196578875	H1-hESC	embryonic stem cell:	n/a	chr1:196577658-196577667 chr1:196578657-196578666 chr1:196578159-196578169
16	TAF1	chr1:196577131-196578857	H1-hESC	embryonic stem cell:	n/a	n/a
17	E2F6	chr1:196577590-196578762	H1-hESC	embryonic stem cell:	n/a	chr1:196578043-196578052
18	CEBPB	chr1:196578488-196578824	K562	blood:	n/a	chr1:196578654-196578665
19	MXI1	chr1:196576771-196579339	SK-N-SH	brain:	n/a	n/a
20	RFX5	chr1:196576790-196579150	SK-N-SH	brain:	n/a	chr1:196578044-196578053
21	KAP1	chr1:196577054-196578853	HEK293	kidney:	n/a	n/a
22	CTBP2	chr1:196577115-196578779	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr1:196577368-196578832	H1-hESC	embryonic stem cell:	n/a	chr1:196577658-196577667 chr1:196578657-196578666 chr1:196578159-196578169
24	CEBPB	chr1:196578451-196578789	A549	lung:	n/a	chr1:196578654-196578665
25	REST	chr1:196577016-196578861	H1-neurons	neurons:	n/a	chr1:196577534-196577541

Variant related genes	Relation type
KCNT2	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10754193	1.00[CEU][hapmap]
rs12128003	1.00[CEU][hapmap]
rs12128544	1.00[CEU][hapmap]
rs13375443	1.00[CEU][hapmap]
rs13375567	1.00[CEU][hapmap]
rs2335906	1.00[CEU][hapmap]
rs4314834	1.00[CEU][hapmap]
rs4507960	1.00[CEU][hapmap]
rs4515738	1.00[CEU][hapmap]
rs4625226	1.00[CEU][hapmap]
rs4658040	1.00[CEU][hapmap]
rs487114	1.00[CEU][hapmap]
rs499807	1.00[CEU][hapmap]
rs512900	1.00[CEU][hapmap]
rs6663649	1.00[CEU][hapmap]
rs7533533	1.00[CEU][hapmap]
rs7540922	1.00[CEU][hapmap]
rs7547724	1.00[CEU][hapmap]
rs7551203	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196574800-196578800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:196575800-196579200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:196576200-196578800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:196576400-196578800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:196576400-196579200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:196576800-196578800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:196576800-196578800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:196576800-196578800	Active TSS	Stomach Smooth Muscle	stomach
9	chr1:196577000-196578800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:196577200-196578800	Active TSS	Fetal Brain Female	brain
11	chr1:196577600-196578800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:196578200-196578800	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr1:196578200-196578800	Enhancers	Gastric	stomach
14	chr1:196578200-196579200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:196578400-196578800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:196578400-196578800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr1:196578400-196578800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:196578400-196578800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:196578400-196578800	Enhancers	Fetal Heart	heart
20	chr1:196578400-196578800	Flanking Active TSS	Fetal Kidney	kidney
21	chr1:196578400-196578800	Active TSS	Fetal Muscle Trunk	muscle
22	chr1:196578400-196578800	Enhancers	A549	lung
23	chr1:196578400-196579000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:196578400-196579000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr1:196578400-196579000	Flanking Active TSS	Liver	Liver
26	chr1:196578400-196579400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:196578600-196578800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:196578600-196578800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:196578600-196578800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:196578600-196578800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:196578600-196578800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:196578600-196578800	Enhancers	Primary hematopoietic stem cells	blood
33	chr1:196578600-196578800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:196578600-196578800	Enhancers	Brain Substantia Nigra	brain
35	chr1:196578600-196578800	Active TSS	Fetal Brain Male	brain
36	chr1:196578600-196578800	Bivalent Enhancer	Fetal Intestine Large	intestine
37	chr1:196578600-196578800	Enhancers	Fetal Muscle Leg	muscle
38	chr1:196578600-196578800	Active TSS	Fetal Thymus	thymus
39	chr1:196578600-196578800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:196578600-196579000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
41	chr1:196578600-196579000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:196578600-196579000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:196578600-196579000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr1:196578600-196579400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr1:196578600-196579600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr1:196578600-196581000	Weak transcription	Psoas Muscle	Psoas

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