Variant report

Variant	rs1144300
Chromosome Location	chr1:95002211-95002212
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	chr1:95001684-95002305	U87	brain:	n/a	n/a
2	POLR2A	chr1:94992567-95005960	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:94991604-95010849	IMR90	lung:	n/a	n/a
4	POLR2A	chr1:95001684-95002362	U87	brain:	n/a	n/a
5	POLR2A	chr1:95000323-95009541	MCF10A-Er-Src	breast:	n/a	n/a
6	CHD1	chr1:94994939-95011321	IMR90	lung:	n/a	n/a
7	POLR2A	chr1:94999692-95008368	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95001173..95003691-chr1:95006398..95009153,2	MCF-7	breast:

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

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1361600	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3761955	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3917615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs762485	1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs841697	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs958587	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]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871764	chr1:94917402-95004084	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1144300	PTBP2	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94956200-95004000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:94958600-95004200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:94965600-95006400	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:94970400-95003800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:94972200-95004400	Weak transcription	A549	lung
6	chr1:94979200-95005000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:94986000-95006200	Weak transcription	Liver	Liver
8	chr1:94991600-95004000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:94993600-95002400	Weak transcription	Stomach Mucosa	stomach
10	chr1:94993600-95002800	Weak transcription	Fetal Brain Male	brain
11	chr1:94993600-95004800	Weak transcription	HSMMtube	muscle
12	chr1:94994000-95003600	Weak transcription	Brain Germinal Matrix	brain
13	chr1:94994000-95003800	Weak transcription	Brain Substantia Nigra	brain
14	chr1:94994200-95002800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:94994400-95005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:94994600-95002400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:94994600-95003800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:94994600-95005200	Weak transcription	Esophagus	oesophagus
19	chr1:94994600-95006200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:94994800-95002400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:94995200-95006200	Weak transcription	Spleen	Spleen
22	chr1:94995600-95002800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:94995600-95003200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:94995600-95003400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:94995800-95002800	Strong transcription	Hela-S3	cervix
26	chr1:94995800-95003000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:94995800-95004000	Strong transcription	HSMM	muscle
28	chr1:94996800-95002600	Weak transcription	Fetal Brain Female	brain
29	chr1:94996800-95005200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:94997600-95005000	Weak transcription	Dnd41	blood
31	chr1:94997600-95005200	Weak transcription	Gastric	stomach
32	chr1:94998000-95004000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:94998200-95004000	Weak transcription	Fetal Kidney	kidney
34	chr1:94999000-95005400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:94999800-95002800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:94999800-95003400	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:95000200-95002600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr1:95000200-95003000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:95000400-95002600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:95000400-95002600	Strong transcription	Colonic Mucosa	Colon
41	chr1:95000400-95003600	Genic enhancers	Placenta Amnion	Placenta Amnion
42	chr1:95000400-95005600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
43	chr1:95000600-95002400	Genic enhancers	NHLF	lung
44	chr1:95000600-95002800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:95000800-95003000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:95000800-95003000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:95001000-95003800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:95001000-95003800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:95001000-95004200	Genic enhancers	HepG2	liver
50	chr1:95001200-95006400	Weak transcription	Small Intestine	intestine

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