Variant report

Variant	rs12142425
Chromosome Location	chr1:196580374-196580375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:196580329-196580379	ProgFib	skin:	n/a
2	chr1:196580329-196580379	SK-N-SH_RA	brain:	n/a
3	chr1:196580329-196580379	AG09309	skin:	n/a
4	chr1:196580329-196580379	Hela-S3	cervix:	n/a
5	chr1:196580329-196580379	SAEC	small airway:	n/a
6	chr1:196580329-196580379	IMR90	lung:	fetal
7	chr1:196580329-196580379	T-47D	breast:	n/a
8	chr1:196580329-196580379	H1-hESC	embryonic stem cell:	embryo
9	chr1:196580329-196580379	NH-A	brain:	n/a
10	chr1:196580329-196580379	SK-N-SH	brain:	n/a
11	chr1:196580329-196580379	HMEC	breast:	n/a
12	chr1:196580329-196580379	NHDF-neo	bronchial:	n/a
13	chr1:196580329-196580379	HEK293	kidney:	embryo
14	chr1:196580329-196580379	AG09319	gingival:	n/a
15	chr1:196580329-196580379	NT2-D1	testis:	n/a
16	chr1:196580329-196580379	ovcar-3	ovarian:	n/a
17	chr1:196580329-196580379	HAEpiC	amniotic membrane:	n/a
18	chr1:196580329-196580379	AG04450	lung:	fetal
19	chr1:196580329-196580379	PrEC	prostate:	n/a
20	chr1:196580329-196580379	SK-N-MC	brain:	n/a
21	chr1:196580329-196580379	GM12878	blood:	n/a
22	chr1:196580329-196580379	HEEpiC	esophagus:	n/a
23	chr1:196580329-196580379	PFSK-1	brain:	n/a
24	chr1:196580329-196580379	BJ	skin:	n/a
25	chr1:196580329-196580379	MCF10A-Er-Src	breast:	n/a
26	chr1:196580329-196580379	GM19239	blood:	n/a
27	chr1:196580329-196580379	HRE	kidney:	n/a
28	chr1:196580329-196580379	PANC-1	pancreas:	n/a
29	chr1:196580329-196580379	HCPEpiC	choroid plexus:	n/a
30	chr1:196580329-196580379	RPTEC	kidney:	n/a
31	chr1:196580329-196580379	HRCEpiC	kidney:	n/a
32	chr1:196580329-196580379	GM12891	blood:	n/a
33	chr1:196580329-196580379	HPAEpiC	pulmonary alveolar:	n/a
34	chr1:196580329-196580379	HNPCEpiC	eye:	n/a
35	chr1:196580329-196580379	HepG2	liver:	n/a
36	chr1:196580329-196580379	Caco-2	colon:	n/a
37	chr1:196580329-196580379	HIPEpiC	eye:	n/a
38	chr1:196580329-196580379	Hepatocyte	liver:	n/a
39	chr1:196580329-196580379	MCF-7	breast:	n/a
40	chr1:196580329-196580379	AG10803	skin:	n/a
41	chr1:196580329-196580379	GM12892	blood:	n/a
42	chr1:196580329-196580379	HCF	heart:	n/a
43	chr1:196580329-196580379	U87	brain:	n/a
44	chr1:196580329-196580379	CMK	blood:	n/a
45	chr1:196580329-196580379	SKMC	muscle:	n/a
46	chr1:196580329-196580379	A549	lung:	n/a
47	chr1:196580329-196580379	HL-60	blood:	n/a
48	chr1:196580329-196580379	HUVEC	blood vessel:	n/a
49	chr1:196580329-196580379	GM06990	blood:	n/a
50	chr1:196580329-196580379	ECC-1	luminal epithelium:	n/a

No data

Variant related genes	Relation type
KCNT2	CpG island

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12127468	0.87[YRI][hapmap];0.92[AFR][1000 genomes]
rs12130043	0.85[AFR][1000 genomes]
rs35196104	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35558539	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35906110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74134347	0.83[AFR][1000 genomes]
rs74134368	0.85[AFR][1000 genomes]
rs74134369	0.85[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:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196578600-196581000	Weak transcription	Psoas Muscle	Psoas
2	chr1:196578800-196580400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:196578800-196580400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:196578800-196581000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:196579000-196580400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:196579000-196581200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:196579000-196581400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:196579400-196580400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:196579400-196580800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:196579400-196581200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr1:196579600-196580600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:196579600-196581200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:196580000-196581400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:196580200-196581400	Enhancers	HUES64 Cell Line	embryonic stem cell

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