Variant report

Variant	rs477992
Chromosome Location	chr1:120257576-120257577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:120254329-120257606	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:120257195-120257587	H1-hESC	embryonic stem cell:	n/a	n/a
3	KAP1	chr1:120255437-120258648	HEK293	kidney:	n/a	n/a
4	ZNF263	chr1:120254121-120257637	HEK293-T-REx	kidney:	n/a	chr1:120254933-120254942 chr1:120255517-120255526 chr1:120254446-120254455
5	POLR2A	chr1:120256807-120257832	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:120254079-120257811	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:120257538-120258511	K562	blood:	n/a	n/a
8	KAP1	chr1:120255379-120257600	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:119682953..119685803-chr1:120256738..120259239,2	K562	blood:
2	chr1:120257304..120259977-chr1:120266897..120269007,2	K562	blood:
3	chr1:120188760..120191651-chr1:120254416..120257641,3	K562	blood:
4	chr1:120188760..120191459-chr1:120254916..120257641,2	K562	blood:

Variant related genes	Relation type
PHGDH	TF binding region
ENSG00000116874	Chromatin interaction
ENSG00000143067	Chromatin interaction
ENSG00000231365	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1163251	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2764886	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs478093	0.91[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs483180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs487081	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs487884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs496195	0.89[ASN][1000 genomes]
rs496198	0.89[ASN][1000 genomes]
rs511059	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs514491	0.89[ASN][1000 genomes]
rs517533	0.89[ASN][1000 genomes]
rs532303	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539708	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs541503	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs561931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[ASN][1000 genomes]
rs592762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs594400	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs595283	0.98[ASN][1000 genomes]
rs597308	0.89[ASN][1000 genomes]
rs598685	0.89[ASN][1000 genomes]
rs606312	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs611365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs612430	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs627707	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs629735	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs637868	0.86[JPT][hapmap]
rs639216	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs639761	0.91[ASN][1000 genomes]
rs640195	0.91[ASN][1000 genomes]
rs658442	0.93[ASN][1000 genomes]
rs660073	0.93[ASN][1000 genomes]
rs662243	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs662602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666930	0.85[CHD][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs677277	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs839600	0.89[ASN][1000 genomes]
rs839605	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs866321	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Metabolic traits	21886157	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs477992	PHGDH	cis	parietal	SCAN
rs477992	C1orf161	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120255600-120257600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:120255600-120257600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:120255600-120258400	Weak transcription	Right Ventricle	heart
4	chr1:120255800-120257600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:120255800-120259400	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr1:120256000-120257600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:120256000-120257600	Enhancers	Placenta	Placenta
8	chr1:120256000-120258800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:120256000-120258800	Enhancers	Ovary	ovary
10	chr1:120256000-120259000	Enhancers	Adipose Nuclei	Adipose
11	chr1:120256000-120259400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
12	chr1:120256000-120263800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:120256200-120257600	Enhancers	Fetal Brain Male	brain
14	chr1:120256200-120258000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:120256200-120259400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:120256200-120266600	Weak transcription	Primary B cells from cord blood	blood
17	chr1:120256200-120267400	Weak transcription	Lung	lung
18	chr1:120256200-120271800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr1:120256400-120258000	Enhancers	Brain Hippocampus Middle	brain
20	chr1:120256400-120258200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:120256400-120258200	Weak transcription	Right Atrium	heart
22	chr1:120256400-120258600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:120256400-120259200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:120256400-120259400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:120256400-120259600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:120256400-120271800	Weak transcription	Gastric	stomach
27	chr1:120256400-120276800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:120256400-120284400	Weak transcription	GM12878-XiMat	blood
29	chr1:120256600-120257600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:120256600-120257600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr1:120256600-120257600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:120256600-120257600	Transcr. at gene 5' and 3'	Hela-S3	cervix
33	chr1:120256600-120258000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:120256600-120263400	Weak transcription	Primary T cells from cord blood	blood
35	chr1:120256600-120275600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr1:120256800-120257600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:120256800-120257600	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr1:120256800-120257800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:120256800-120258000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:120256800-120258600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:120256800-120263800	Weak transcription	HUVEC	blood vessel
42	chr1:120256800-120266000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:120257000-120257600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:120257000-120257600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr1:120257000-120258200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:120257000-120258200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr1:120257000-120258200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:120257000-120258200	Weak transcription	Esophagus	oesophagus
49	chr1:120257000-120258200	Enhancers	Fetal Kidney	kidney
50	chr1:120257000-120258200	Weak transcription	Fetal Thymus	thymus

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