Variant report

Variant	rs12057776
Chromosome Location	chr1:120262152-120262153
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	chr1:120261710-120262180	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:120262137-120262828	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PHGDH	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10802132	0.84[ASN][1000 genomes]
rs10802133	0.84[ASN][1000 genomes]
rs1406917	0.82[ASN][1000 genomes]
rs1886736	0.90[ASN][1000 genomes]
rs2236398	0.87[ASN][1000 genomes]
rs28501188	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3790708	0.94[ASN][1000 genomes]
rs6428840	0.80[ASN][1000 genomes]
rs894079	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs942835	0.89[AFR][1000 genomes];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

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120256000-120263800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr1:120256200-120266600	Weak transcription	Primary B cells from cord blood	blood
3	chr1:120256200-120267400	Weak transcription	Lung	lung
4	chr1:120256200-120271800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr1:120256400-120271800	Weak transcription	Gastric	stomach
6	chr1:120256400-120276800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:120256400-120284400	Weak transcription	GM12878-XiMat	blood
8	chr1:120256600-120263400	Weak transcription	Primary T cells from cord blood	blood
9	chr1:120256600-120275600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:120256800-120263800	Weak transcription	HUVEC	blood vessel
11	chr1:120256800-120266000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:120257000-120263800	Weak transcription	Aorta	Aorta
13	chr1:120257000-120266000	Weak transcription	HSMMtube	muscle
14	chr1:120257000-120271800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:120257000-120277400	Weak transcription	Fetal Heart	heart
16	chr1:120257000-120278400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:120257000-120278600	Weak transcription	HSMM	muscle
18	chr1:120257000-120282400	Weak transcription	A549	lung
19	chr1:120257200-120263200	Weak transcription	NHLF	lung
20	chr1:120257200-120287000	Weak transcription	NH-A	brain
21	chr1:120257600-120263600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:120257600-120263600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:120257600-120263800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:120257600-120264400	Weak transcription	Placenta	Placenta
25	chr1:120257600-120268000	Weak transcription	Fetal Brain Male	brain
26	chr1:120258600-120263200	Weak transcription	HMEC	breast
27	chr1:120258600-120263400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:120258600-120263800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:120258600-120267200	Weak transcription	Fetal Brain Female	brain
30	chr1:120258600-120289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:120258800-120263200	Weak transcription	Thymus	Thymus
32	chr1:120258800-120263400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:120258800-120263800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:120258800-120266000	Weak transcription	Esophagus	oesophagus
35	chr1:120258800-120269400	Weak transcription	Spleen	Spleen
36	chr1:120258800-120275000	Weak transcription	Right Atrium	heart
37	chr1:120259000-120262200	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:120259000-120262800	Weak transcription	Adipose Nuclei	Adipose
39	chr1:120259000-120263400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:120259000-120263400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:120259000-120263400	Weak transcription	Fetal Thymus	thymus
42	chr1:120259000-120265800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr1:120259200-120262200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:120259200-120262400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:120259200-120262600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:120259200-120262800	Weak transcription	Fetal Lung	lung
47	chr1:120259200-120263200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:120259200-120263800	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:120259200-120263800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:120259200-120264000	Weak transcription	Brain Germinal Matrix	brain

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