Variant report

Variant	rs454510
Chromosome Location	chr1:120195042-120195043
allele	A/G
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:3)
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	chr1:120195038-120195088	SK-N-MC	brain:	n/a
2	chr1:120195038-120195088	NT2-D1	testis:	n/a
3	chr1:120195038-120195088	Hela-S3	cervix:	n/a
4	chr1:120195038-120195088	Jurkat	blood:	n/a
5	chr1:120195038-120195088	NHDF-neo	bronchial:	n/a
6	chr1:120195038-120195088	SKMC	muscle:	n/a
7	chr1:120195038-120195088	ProgFib	skin:	n/a
8	chr1:120195038-120195088	HRPEpiC	eye:	n/a
9	chr1:120195038-120195088	NH-A	brain:	n/a
10	chr1:120195038-120195088	GM12891	blood:	n/a
11	chr1:120195038-120195088	GM12878	blood:	n/a
12	chr1:120195038-120195088	SK-N-SH	brain:	n/a
13	chr1:120195038-120195088	CMK	blood:	n/a
14	chr1:120195038-120195088	HMEC	breast:	n/a
15	chr1:120195038-120195088	AG09319	gingival:	n/a
16	chr1:120195038-120195088	Hepatocyte	liver:	n/a
17	chr1:120195038-120195088	BJ	skin:	n/a
18	chr1:120195038-120195088	ECC-1	luminal epithelium:	n/a
19	chr1:120195038-120195088	PrEC	prostate:	n/a
20	chr1:120195038-120195088	AG04450	lung:	fetal
21	chr1:120195038-120195088	K562	blood:	n/a
22	chr1:120195038-120195088	HRCEpiC	kidney:	n/a
23	chr1:120195038-120195088	AG04449	skin:	fetal
24	chr1:120195038-120195088	AG09309	skin:	n/a
25	chr1:120195038-120195088	NB4	blood:	n/a
26	chr1:120195038-120195088	H1-hESC	embryonic stem cell:	embryo
27	chr1:120195038-120195088	PANC-1	pancreas:	n/a
28	chr1:120195038-120195088	SAEC	small airway:	n/a
29	chr1:120195038-120195088	HRE	kidney:	n/a
30	chr1:120195038-120195088	NHBE	bronchial:	n/a
31	chr1:120195038-120195088	HIPEpiC	eye:	n/a
32	chr1:120195038-120195088	GM06990	blood:	n/a
33	chr1:120195038-120195088	IMR90	lung:	fetal
34	chr1:120195038-120195088	RPTEC	kidney:	n/a
35	chr1:120195038-120195088	AoSMC	blood vessel:	n/a
36	chr1:120195038-120195088	HAEpiC	amniotic membrane:	n/a
37	chr1:120195038-120195088	MCF-7	breast:	n/a
38	chr1:120195038-120195088	AG10803	skin:	n/a
39	chr1:120195038-120195088	HEEpiC	esophagus:	n/a
40	chr1:120195038-120195088	T-47D	breast:	n/a
41	chr1:120195038-120195088	HepG2	liver:	n/a
42	chr1:120195038-120195088	PFSK-1	brain:	n/a
43	chr1:120195038-120195088	A549	lung:	n/a
44	chr1:120195038-120195088	GM19239	blood:	n/a
45	chr1:120195038-120195088	HCF	heart:	n/a
46	chr1:120195038-120195088	GM12892	blood:	n/a
47	chr1:120195038-120195088	HPAEpiC	pulmonary alveolar:	n/a
48	chr1:120195038-120195088	Caco-2	colon:	n/a
49	chr1:120195038-120195088	HL-60	blood:	n/a
50	chr1:120195038-120195088	ovcar-3	ovarian:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr1:120192852..120195358-chr1:120195799..120197407,2	K562	blood:
2	chr1:120193408..120195827-chr1:120201607..120203462,2	K562	blood:
3	chr1:120188687..120197065-chr1:120197482..120205927,19	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF697	CpG island
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs347903	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs347904	0.89[JPT][hapmap]
rs372814	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs376910	0.80[GIH][hapmap];0.90[JPT][hapmap]
rs377033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422647	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496886	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs539799	0.90[JPT][hapmap]
rs838986	0.90[JPT][hapmap]
rs838989	0.80[GIH][hapmap];0.90[JPT][hapmap]
rs838990	0.89[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2757749	chr1:120016696-120214577	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2758964	chr1:120016696-120214577	Enhancers ZNF genes & repeats Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs454510	PHGDH	cis	multi-tissue	Pritchard
rs454510	ATP1A1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120191600-120202200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:120191800-120196000	Weak transcription	Adipose Nuclei	Adipose
3	chr1:120191800-120196200	Weak transcription	Ovary	ovary
4	chr1:120191800-120198600	Weak transcription	Placenta	Placenta
5	chr1:120192000-120195600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:120192000-120195800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:120192000-120196000	Weak transcription	Liver	Liver
8	chr1:120192000-120196000	Weak transcription	NHLF	lung
9	chr1:120192000-120196200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:120192000-120196800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:120192000-120198000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:120192000-120198000	Weak transcription	Fetal Stomach	stomach
13	chr1:120193400-120195200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:120193400-120195600	Enhancers	HMEC	breast
15	chr1:120193400-120195600	Enhancers	NHEK	skin
16	chr1:120193600-120202400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:120193800-120195400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:120193800-120195400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:120193800-120195400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:120194000-120195200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:120194000-120196000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:120194000-120197800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:120194000-120198800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:120194000-120200200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:120194400-120195200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr1:120194600-120198600	Weak transcription	GM12878-XiMat	blood
27	chr1:120194800-120202000	Weak transcription	Fetal Intestine Small	intestine
28	chr1:120195000-120196200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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