Variant report

Variant	rs4907956
Chromosome Location	chr1:102312703-102312704
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:102312562-102312746	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr1:102312412-102312775	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr1:102312302-102312786	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr1:102312260-102312742	H1-hESC	embryonic stem cell:	n/a	n/a
5	TBP	chr1:102312390-102312749	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:102312671-102312721	HEEpiC	esophagus:	n/a
2	chr1:102312671-102312721	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:102312671-102312721	HCPEpiC	choroid plexus:	n/a
4	chr1:102312671-102312721	HRE	kidney:	n/a
5	chr1:102312671-102312721	Hela-S3	cervix:	n/a
6	chr1:102312671-102312721	HMEC	breast:	n/a
7	chr1:102312671-102312721	K562	blood:	n/a
8	chr1:102312671-102312721	GM12878	blood:	n/a
9	chr1:102312671-102312721	HCF	heart:	n/a
10	chr1:102312671-102312721	SAEC	small airway:	n/a
11	chr1:102312671-102312721	T-47D	breast:	n/a
12	chr1:102312671-102312721	HEK293	kidney:	embryo
13	chr1:102312671-102312721	ProgFib	skin:	n/a
14	chr1:102312671-102312721	Caco-2	colon:	n/a
15	chr1:102312671-102312721	SK-N-SH_RA	brain:	n/a
16	chr1:102312671-102312721	HL-60	blood:	n/a
17	chr1:102312671-102312721	HAEpiC	amniotic membrane:	n/a
18	chr1:102312671-102312721	HepG2	liver:	n/a
19	chr1:102312671-102312721	AG10803	skin:	n/a
20	chr1:102312671-102312721	GM12892	blood:	n/a
21	chr1:102312671-102312721	NB4	blood:	n/a
22	chr1:102312671-102312721	A549	lung:	n/a
23	chr1:102312671-102312721	SK-N-MC	brain:	n/a
24	chr1:102312671-102312721	NHBE	bronchial:	n/a
25	chr1:102312671-102312721	IMR90	lung:	fetal
26	chr1:102312671-102312721	HUVEC	blood vessel:	n/a
27	chr1:102312671-102312721	AG04449	skin:	fetal
28	chr1:102312671-102312721	GM19239	blood:	n/a
29	chr1:102312671-102312721	GM12891	blood:	n/a
30	chr1:102312671-102312721	HRPEpiC	eye:	n/a
31	chr1:102312671-102312721	NHDF-neo	bronchial:	n/a
32	chr1:102312671-102312721	PANC-1	pancreas:	n/a
33	chr1:102312671-102312721	H1-hESC	embryonic stem cell:	embryo
34	chr1:102312671-102312721	LNCaP	prostate:	n/a
35	chr1:102312671-102312721	AG09319	gingival:	n/a
36	chr1:102312671-102312721	PFSK-1	brain:	n/a
37	chr1:102312671-102312721	BJ	skin:	n/a
38	chr1:102312671-102312721	ovcar-3	ovarian:	n/a
39	chr1:102312671-102312721	MCF-7	breast:	n/a
40	chr1:102312671-102312721	ECC-1	luminal epithelium:	n/a
41	chr1:102312671-102312721	CMK	blood:	n/a
42	chr1:102312671-102312721	GM06990	blood:	n/a
43	chr1:102312671-102312721	HCM	heart:	n/a
44	chr1:102312671-102312721	AG04450	lung:	fetal
45	chr1:102312671-102312721	AG09309	skin:	n/a
46	chr1:102312671-102312721	HCT-116	colon:	n/a
47	chr1:102312671-102312721	U87	brain:	n/a
48	chr1:102312671-102312721	Jurkat	blood:	n/a
49	chr1:102312671-102312721	Hepatocyte	liver:	n/a
50	chr1:102312671-102312721	SK-N-SH	brain:	n/a

No data

Variant related genes	Relation type
OLFM3	TF binding region
OLFM3	CpG island

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1415099	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1539091	1.00[CHB][hapmap]
rs1577717	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17430580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17431961	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs17470860	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1856037	1.00[CHB][hapmap]
rs6682150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6694948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6695052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7536632	1.00[CHB][hapmap]
rs9943151	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9943277	0.90[AMR][1000 genomes];0.97[EUR][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	nsv522921	chr1:102170295-102876392	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv522156	chr1:102309649-102421714	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4907956	AMY2B	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:102311000-102313000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:102311200-102313400	Active TSS	Fetal Intestine Large	intestine
3	chr1:102311400-102313400	Active TSS	Fetal Intestine Small	intestine
4	chr1:102312200-102312800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:102312200-102312800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:102312200-102312800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr1:102312200-102312800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:102312200-102312800	Active TSS	Fetal Kidney	kidney
9	chr1:102312200-102313000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:102312200-102313000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:102312200-102313000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:102312400-102312800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
13	chr1:102312400-102312800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:102312400-102312800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:102312400-102312800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:102312400-102312800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:102312400-102312800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr1:102312400-102312800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:102312400-102312800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:102312400-102312800	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr1:102312400-102312800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:102312400-102312800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:102312400-102312800	Active TSS	Brain Angular Gyrus	brain
24	chr1:102312400-102312800	Active TSS	Brain Anterior Caudate	brain
25	chr1:102312400-102312800	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr1:102312400-102312800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:102312400-102312800	Bivalent Enhancer	Esophagus	oesophagus
28	chr1:102312400-102312800	Enhancers	Fetal Brain Male	brain
29	chr1:102312400-102312800	Flanking Active TSS	Fetal Brain Female	brain
30	chr1:102312400-102312800	Enhancers	Fetal Lung	lung
31	chr1:102312400-102312800	Active TSS	Fetal Stomach	stomach
32	chr1:102312400-102312800	Enhancers	Gastric	stomach
33	chr1:102312400-102312800	Flanking Bivalent TSS/Enh	Left Ventricle	heart
34	chr1:102312400-102312800	Enhancers	Pancreas	Pancrea
35	chr1:102312400-102312800	Enhancers	Right Atrium	heart
36	chr1:102312400-102313000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr1:102312400-102313600	Enhancers	Fetal Heart	heart
38	chr1:102312600-102312800	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr1:102312600-102313000	Active TSS	Brain Inferior Temporal Lobe	brain

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