Variant report

Variant	rs3796242
Chromosome Location	chr3:150690439-150690440
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr3:150690429-150690698	Hela-S3	cervix:	n/a	n/a
2	REST	chr3:150690369-150690748	HepG2	liver:	n/a	n/a
3	REST	chr3:150690387-150690827	ECC-1	luminal epithelium:	n/a	n/a
4	REST	chr3:150690407-150690792	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr3:150690406-150690789	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chr3:150690381-150690700	PFSK-1	brain:	n/a	n/a
7	REST	chr3:150690437-150690752	HL-60	blood:	n/a	n/a
8	REST	chr3:150690401-150690698	GM12878	blood:	n/a	n/a
9	REST	chr3:150690335-150690787	ECC-1	luminal epithelium:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:150690403-150690453	SKMC	muscle:	n/a
2	chr3:150690429-150690479	NB4	blood:	n/a
3	chr3:150690429-150690479	SKMC	muscle:	n/a
4	chr3:150690403-150690453	AoSMC	blood vessel:	n/a
5	chr3:150690403-150690453	HEEpiC	esophagus:	n/a
6	chr3:150690429-150690479	A549	lung:	n/a
7	chr3:150690403-150690453	IMR90	lung:	fetal
8	chr3:150690429-150690479	HIPEpiC	eye:	n/a
9	chr3:150690403-150690453	T-47D	breast:	n/a
10	chr3:150690429-150690479	ProgFib	skin:	n/a
11	chr3:150690403-150690453	CMK	blood:	n/a
12	chr3:150690429-150690479	NHDF-neo	bronchial:	n/a
13	chr3:150690403-150690453	HAEpiC	amniotic membrane:	n/a
14	chr3:150690403-150690453	HCF	heart:	n/a
15	chr3:150690429-150690479	HCT-116	colon:	n/a
16	chr3:150690429-150690479	HRE	kidney:	n/a
17	chr3:150690429-150690479	SAEC	small airway:	n/a
18	chr3:150690429-150690479	GM06990	blood:	n/a
19	chr3:150690403-150690453	AG10803	skin:	n/a
20	chr3:150690403-150690453	AG04449	skin:	fetal
21	chr3:150690403-150690453	GM06990	blood:	n/a
22	chr3:150690429-150690479	HEK293	kidney:	embryo
23	chr3:150690429-150690479	HRPEpiC	eye:	n/a
24	chr3:150690403-150690453	MCF-7	breast:	n/a
25	chr3:150690403-150690453	BJ	skin:	n/a
26	chr3:150690429-150690479	HEEpiC	esophagus:	n/a
27	chr3:150690429-150690479	HMEC	breast:	n/a
28	chr3:150690403-150690453	A549	lung:	n/a
29	chr3:150690429-150690479	Hepatocyte	liver:	n/a
30	chr3:150690403-150690453	HPAEpiC	pulmonary alveolar:	n/a
31	chr3:150690429-150690479	HAEpiC	amniotic membrane:	n/a
32	chr3:150690429-150690479	Caco-2	colon:	n/a
33	chr3:150690403-150690453	U87	brain:	n/a
34	chr3:150690403-150690453	GM12891	blood:	n/a
35	chr3:150690429-150690479	PrEC	prostate:	n/a
36	chr3:150690429-150690479	HPAEpiC	pulmonary alveolar:	n/a
37	chr3:150690403-150690453	PFSK-1	brain:	n/a
38	chr3:150690429-150690479	MCF-7	breast:	n/a
39	chr3:150690403-150690453	AG09309	skin:	n/a
40	chr3:150690403-150690453	Hela-S3	cervix:	n/a
41	chr3:150690403-150690453	Jurkat	blood:	n/a
42	chr3:150690403-150690453	HIPEpiC	eye:	n/a
43	chr3:150690429-150690479	IMR90	lung:	fetal
44	chr3:150690429-150690479	PFSK-1	brain:	n/a
45	chr3:150690403-150690453	HRCEpiC	kidney:	n/a
46	chr3:150690429-150690479	GM12892	blood:	n/a
47	chr3:150690403-150690453	HepG2	liver:	n/a
48	chr3:150690429-150690479	K562	blood:	n/a
49	chr3:150690429-150690479	CMK	blood:	n/a
50	chr3:150690403-150690453	HRE	kidney:	n/a

No data

Variant related genes	Relation type
CLRN1-AS1	TF binding region
CLRN1-AS1	CpG island

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12107625	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12107635	0.81[EUR][1000 genomes]
rs12485344	0.84[EUR][1000 genomes]
rs12497559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16863118	0.82[EUR][1000 genomes]
rs16863121	0.84[EUR][1000 genomes]
rs1876746	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4434182	0.82[EUR][1000 genomes]
rs61104836	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62282747	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62282751	0.82[EUR][1000 genomes]
rs62282752	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62282753	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62284766	0.84[EUR][1000 genomes]
rs744669	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs744670	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7617623	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625786	0.81[EUR][1000 genomes]
rs7625985	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7647641	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915879	chr3:150607390-150860207	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150686800-150690600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:150688000-150691000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr3:150688200-150691000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:150688600-150690800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:150689200-150691000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:150689400-150690600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr3:150689400-150691000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr3:150689600-150691000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr3:150689800-150691800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:150690000-150690600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:150690000-150690800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:150690000-150690800	Active TSS	Duodenum Mucosa	Duodenum
13	chr3:150690000-150691000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:150690000-150694600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:150690200-150690600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:150690200-150690600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:150690200-150690600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:150690200-150690600	Enhancers	Placenta	Placenta
19	chr3:150690200-150690600	Enhancers	Pancreas	Pancrea
20	chr3:150690200-150690800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:150690200-150690800	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr3:150690200-150691000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr3:150690400-150690600	Active TSS	Fetal Intestine Large	intestine
24	chr3:150690400-150690800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr3:150690400-150691000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:150690400-150693200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:150690400-150694000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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