Variant report

Variant	rs667770
Chromosome Location	chr1:120259154-120259155
allele	C/T
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	chr1:120259098-120259420	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:120258112-120259607	Hela-S3	cervix:	n/a	n/a
3	ZNF263	chr1:120258058-120259405	HEK293-T-REx	kidney:	n/a	chr1:120258332-120258353
4	POLR2A	chr1:120259099-120259336	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:120258147-120259285	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:120257819-120259532	H1-hESC	embryonic stem cell:	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	chr1:120258475..120260260-chr1:120263404..120265007,2	K562	blood:
4	chr1:120189290..120192192-chr1:120258102..120260904,2	K562	blood:

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

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10923887	0.85[EUR][1000 genomes]
rs380155	0.84[MEX][hapmap]
rs481357	0.90[JPT][hapmap]
rs541763	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550174	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573763	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs586650	0.91[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.94[ASN][1000 genomes]
rs598100	0.95[JPT][hapmap]
rs620741	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs636101	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs646124	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs663807	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs839613	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs839615	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs839616	0.94[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs667770	PHGDH	cis	multi-tissue	Pritchard
rs667770	CD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120255800-120259400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr1:120256000-120259400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
3	chr1:120256000-120263800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr1:120256200-120259400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:120256200-120266600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:120256200-120267400	Weak transcription	Lung	lung
7	chr1:120256200-120271800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:120256400-120259200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:120256400-120259400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:120256400-120259600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:120256400-120271800	Weak transcription	Gastric	stomach
12	chr1:120256400-120276800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:120256400-120284400	Weak transcription	GM12878-XiMat	blood
14	chr1:120256600-120263400	Weak transcription	Primary T cells from cord blood	blood
15	chr1:120256600-120275600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:120256800-120263800	Weak transcription	HUVEC	blood vessel
17	chr1:120256800-120266000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:120257000-120259200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:120257000-120259200	Enhancers	Colon Smooth Muscle	Colon
20	chr1:120257000-120259400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr1:120257000-120259600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr1:120257000-120259600	Enhancers	Pancreas	Pancrea
23	chr1:120257000-120259800	Enhancers	Liver	Liver
24	chr1:120257000-120263800	Weak transcription	Aorta	Aorta
25	chr1:120257000-120266000	Weak transcription	HSMMtube	muscle
26	chr1:120257000-120271800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:120257000-120277400	Weak transcription	Fetal Heart	heart
28	chr1:120257000-120278400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:120257000-120278600	Weak transcription	HSMM	muscle
30	chr1:120257000-120282400	Weak transcription	A549	lung
31	chr1:120257200-120259200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:120257200-120259200	Enhancers	Fetal Lung	lung
33	chr1:120257200-120259200	Enhancers	K562	blood
34	chr1:120257200-120259400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:120257200-120259400	Enhancers	Fetal Intestine Large	intestine
36	chr1:120257200-120263200	Weak transcription	NHLF	lung
37	chr1:120257200-120287000	Weak transcription	NH-A	brain
38	chr1:120257400-120259200	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:120257400-120259400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:120257400-120259600	Genic enhancers	H1 Cell Line	embryonic stem cell
41	chr1:120257400-120259600	Enhancers	Brain Cingulate Gyrus	brain
42	chr1:120257600-120259400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:120257600-120259400	Enhancers	Brain Anterior Caudate	brain
44	chr1:120257600-120259400	Enhancers	Brain Substantia Nigra	brain
45	chr1:120257600-120262000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:120257600-120263600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:120257600-120263600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:120257600-120263800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:120257600-120264400	Weak transcription	Placenta	Placenta
50	chr1:120257600-120268000	Weak transcription	Fetal Brain Male	brain

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