Variant report

Variant	rs28897764
Chromosome Location	chr3:142281298-142281299
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	GATA3	chr3:142281213-142281413	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:21671785..21672442-chr3:142280767..142281658,2	NB4	blood:
2	chr3:142280626..142282527-chr3:142296623..142299039,2	K562	blood:
3	chr3:142280626..142283157-chr3:142296079..142299039,3	K562	blood:

Variant related genes	Relation type
ATR	TF binding region
ENSG00000175054	Chromatin interaction
ENSG00000117298	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1804758	1.00[JPT][hapmap]
rs28897765	1.00[GIH][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28910270	1.00[CEU][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28910271	1.00[GIH][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28910272	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34104088	1.00[EUR][1000 genomes]
rs34213965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34383865	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34678750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34686786	1.00[AMR][1000 genomes]
rs35264204	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35363608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35404216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35440390	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35988759	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35993426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36090479	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7618253	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28897764	PLS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142226000-142287200	Weak transcription	Right Ventricle	heart
3	chr3:142231600-142295800	Weak transcription	Small Intestine	intestine
4	chr3:142240800-142281600	Weak transcription	Fetal Brain Male	brain
5	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart
6	chr3:142248400-142287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:142253400-142284800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:142253400-142284800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:142253800-142296400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:142256200-142283600	Weak transcription	Aorta	Aorta
11	chr3:142259800-142285600	Strong transcription	Dnd41	blood
12	chr3:142263000-142285400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:142263400-142286200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr3:142263600-142288000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:142263800-142285600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:142263800-142286600	Strong transcription	Liver	Liver
17	chr3:142264000-142285200	Strong transcription	Fetal Thymus	thymus
18	chr3:142265200-142285000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr3:142265200-142287600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:142265400-142283600	Weak transcription	HSMMtube	muscle
21	chr3:142266400-142285600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:142267000-142286600	Strong transcription	Primary B cells from cord blood	blood
23	chr3:142267600-142282000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:142267800-142285200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:142268800-142284200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:142269200-142292600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:142270000-142287200	Weak transcription	Pancreas	Pancrea
28	chr3:142270200-142285000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:142270800-142285200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:142270800-142286400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:142271000-142285400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:142271800-142282200	Weak transcription	Fetal Kidney	kidney
33	chr3:142271800-142285200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:142272200-142286200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:142272400-142282200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:142272600-142282000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:142272600-142283600	Weak transcription	Fetal Brain Female	brain
38	chr3:142272600-142284800	Weak transcription	HepG2	liver
39	chr3:142272600-142287400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:142272600-142296200	Weak transcription	Brain Angular Gyrus	brain
41	chr3:142272600-142296200	Weak transcription	Psoas Muscle	Psoas
42	chr3:142272800-142293400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:142274000-142284800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:142274000-142285200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:142274000-142286600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr3:142274000-142287200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:142274000-142287400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:142274000-142287400	Weak transcription	Gastric	stomach
49	chr3:142274000-142287400	Weak transcription	Lung	lung
50	chr3:142274200-142285000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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