Variant report

Variant	rs838990
Chromosome Location	chr1:120193252-120193253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10494228	0.80[JPT][hapmap]
rs10754417	0.80[JPT][hapmap]
rs347903	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs347904	0.89[JPT][hapmap]
rs347911	0.82[GIH][hapmap];0.84[MEX][hapmap]
rs376910	0.90[JPT][hapmap]
rs377033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs422647	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs454510	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]
rs496886	0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs539799	0.90[JPT][hapmap]
rs838986	0.90[JPT][hapmap]
rs838989	0.90[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs838990	PHGDH	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120191600-120193800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:120191600-120194200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:120191600-120202200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:120191800-120193400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:120191800-120193400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:120191800-120193400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:120191800-120193400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:120191800-120193400	Weak transcription	NHEK	skin
9	chr1:120191800-120196000	Weak transcription	Adipose Nuclei	Adipose
10	chr1:120191800-120196200	Weak transcription	Ovary	ovary
11	chr1:120191800-120198600	Weak transcription	Placenta	Placenta
12	chr1:120192000-120193400	Weak transcription	HMEC	breast
13	chr1:120192000-120193800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:120192000-120193800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:120192000-120193800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:120192000-120193800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:120192000-120194000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:120192000-120194200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:120192000-120195000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:120192000-120195600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:120192000-120195800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:120192000-120196000	Weak transcription	Liver	Liver
23	chr1:120192000-120196000	Weak transcription	NHLF	lung
24	chr1:120192000-120196200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:120192000-120196800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:120192000-120198000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:120192000-120198000	Weak transcription	Fetal Stomach	stomach
28	chr1:120192800-120193800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
29	chr1:120193000-120193600	Enhancers	H1 Cell Line	embryonic stem cell
30	chr1:120193200-120193400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:120193200-120194000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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