Variant report

Variant	rs59786100
Chromosome Location	chr1:196578907-196578908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr1:196576883-196578976	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:196576870-196579084	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD1	chr1:196576411-196579113	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr1:196578456-196579000	IMR90	lung:	n/a	chr1:196578654-196578665
5	CHD2	chr1:196577189-196578907	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr1:196576771-196579339	SK-N-SH	brain:	n/a	n/a
7	RFX5	chr1:196576790-196579150	SK-N-SH	brain:	n/a	chr1:196578044-196578053

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:196578863-196578913	ovcar-3	ovarian:	n/a
2	chr1:196578863-196578913	PANC-1	pancreas:	n/a
3	chr1:196578863-196578913	GM06990	blood:	n/a
4	chr1:196578863-196578913	BE2_C	brain:	n/a
5	chr1:196578863-196578913	K562	blood:	n/a
6	chr1:196578863-196578913	AG09319	gingival:	n/a
7	chr1:196578863-196578913	HRCEpiC	kidney:	n/a
8	chr1:196578863-196578913	AG04449	skin:	fetal
9	chr1:196578863-196578913	HAEpiC	amniotic membrane:	n/a
10	chr1:196578863-196578913	SAEC	small airway:	n/a
11	chr1:196578863-196578913	CMK	blood:	n/a
12	chr1:196578863-196578913	HEK293	kidney:	embryo
13	chr1:196578863-196578913	PrEC	prostate:	n/a
14	chr1:196578863-196578913	GM19239	blood:	n/a
15	chr1:196578863-196578913	BJ	skin:	n/a
16	chr1:196578863-196578913	U87	brain:	n/a
17	chr1:196578863-196578913	HCM	heart:	n/a
18	chr1:196578863-196578913	ECC-1	luminal epithelium:	n/a
19	chr1:196578863-196578913	IMR90	lung:	fetal
20	chr1:196578863-196578913	GM12892	blood:	n/a
21	chr1:196578863-196578913	NHBE	bronchial:	n/a
22	chr1:196578863-196578913	A549	lung:	n/a
23	chr1:196578863-196578913	SKMC	muscle:	n/a
24	chr1:196578863-196578913	NT2-D1	testis:	n/a
25	chr1:196578863-196578913	HNPCEpiC	eye:	n/a
26	chr1:196578863-196578913	SK-N-MC	brain:	n/a
27	chr1:196578863-196578913	HCF	heart:	n/a
28	chr1:196578863-196578913	HMEC	breast:	n/a
29	chr1:196578863-196578913	HepG2	liver:	n/a
30	chr1:196578863-196578913	GM12891	blood:	n/a
31	chr1:196578863-196578913	HUVEC	blood vessel:	n/a
32	chr1:196578863-196578913	Hepatocyte	liver:	n/a
33	chr1:196578863-196578913	H1-hESC	embryonic stem cell:	embryo
34	chr1:196578863-196578913	GM12878	blood:	n/a
35	chr1:196578863-196578913	AG09309	skin:	n/a
36	chr1:196578863-196578913	NH-A	brain:	n/a
37	chr1:196578863-196578913	LNCaP	prostate:	n/a
38	chr1:196578863-196578913	AoSMC	blood vessel:	n/a
39	chr1:196578863-196578913	Hela-S3	cervix:	n/a
40	chr1:196578863-196578913	HRPEpiC	eye:	n/a
41	chr1:196578863-196578913	PFSK-1	brain:	n/a
42	chr1:196578863-196578913	MCF10A-Er-Src	breast:	n/a
43	chr1:196578863-196578913	AG04450	lung:	fetal
44	chr1:196578863-196578913	HEEpiC	esophagus:	n/a
45	chr1:196578863-196578913	HPAEpiC	pulmonary alveolar:	n/a
46	chr1:196578863-196578913	SK-N-SH	brain:	n/a
47	chr1:196578863-196578913	RPTEC	kidney:	n/a
48	chr1:196578863-196578913	HCPEpiC	choroid plexus:	n/a
49	chr1:196578863-196578913	Caco-2	colon:	n/a
50	chr1:196578863-196578913	HRE	kidney:	n/a

No data

Variant related genes	Relation type
KCNT2	TF binding region
KCNT2	CpG island

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs59339468	0.81[AFR][1000 genomes]

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:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196575800-196579200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:196576400-196579200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:196578200-196579200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:196578400-196579000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:196578400-196579000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:196578400-196579000	Flanking Active TSS	Liver	Liver
7	chr1:196578400-196579400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:196578600-196579000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
9	chr1:196578600-196579000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:196578600-196579000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:196578600-196579000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:196578600-196579400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:196578600-196579600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:196578600-196581000	Weak transcription	Psoas Muscle	Psoas
15	chr1:196578800-196579000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:196578800-196579000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:196578800-196579200	Enhancers	Fetal Brain Male	brain
18	chr1:196578800-196579400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:196578800-196579600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:196578800-196580400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:196578800-196580400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:196578800-196581000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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