Variant report

Variant	rs958587
Chromosome Location	chr1:95009145-95009146
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	chr1:94991604-95010849	IMR90	lung:	n/a	n/a
2	POLR2A	chr1:95000323-95009541	MCF10A-Er-Src	breast:	n/a	n/a
3	CHD1	chr1:94994939-95011321	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:95007807..95010747-chr1:95056056..95057592,2	MCF-7	breast:
2	chr1:95001173..95003691-chr1:95006398..95009153,2	MCF-7	breast:
3	chr1:95007807..95010270-chr1:95025313..95026976,2	MCF-7	breast:

Variant related genes	Relation type
F3	TF binding region
ENSG00000117525	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1144300	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1361600	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3761955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3917615	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs762485	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs841697	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs958587	PTBP2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95006800-95009200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:95007000-95009400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:95007200-95009600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:95007400-95009400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:95007600-95010400	Flanking Active TSS	HMEC	breast
6	chr1:95008000-95010600	Enhancers	HSMMtube	muscle
7	chr1:95008200-95009200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:95008200-95009600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:95008200-95009600	Weak transcription	Gastric	stomach
10	chr1:95008200-95011000	Enhancers	HSMM	muscle
11	chr1:95008200-95015600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:95008200-95015600	Weak transcription	Pancreas	Pancrea
13	chr1:95008200-95018000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:95008200-95019800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:95008400-95009200	Weak transcription	Psoas Muscle	Psoas
16	chr1:95008400-95010000	Weak transcription	Right Ventricle	heart
17	chr1:95008400-95010200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:95008400-95010400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:95008400-95010400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:95008400-95010600	Enhancers	Stomach Mucosa	stomach
21	chr1:95008400-95011800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:95008600-95009200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:95008600-95009600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:95008600-95009600	Weak transcription	Aorta	Aorta
25	chr1:95008600-95010200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:95008600-95010400	Flanking Active TSS	NHLF	lung
27	chr1:95008600-95010600	Flanking Active TSS	NHEK	skin
28	chr1:95008600-95011200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:95008800-95009200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:95008800-95009200	Enhancers	Dnd41	blood
31	chr1:95008800-95009400	Weak transcription	Ovary	ovary
32	chr1:95008800-95009600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:95008800-95009600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:95008800-95009600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr1:95008800-95009600	Enhancers	Adipose Nuclei	Adipose
36	chr1:95008800-95009600	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:95008800-95009800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr1:95008800-95010400	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr1:95008800-95010800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:95008800-95011000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr1:95008800-95011200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:95008800-95011200	Enhancers	NH-A	brain
43	chr1:95008800-95011200	Enhancers	Osteobl	bone
44	chr1:95008800-95011600	Enhancers	Hela-S3	cervix
45	chr1:95008800-95014800	Weak transcription	HepG2	liver
46	chr1:95008800-95015000	Weak transcription	Fetal Kidney	kidney
47	chr1:95008800-95015600	Weak transcription	Esophagus	oesophagus
48	chr1:95008800-95015600	Weak transcription	Placenta	Placenta
49	chr1:95008800-95016600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:95009000-95009200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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