Variant report

Variant	rs3761955
Chromosome Location	chr1:95008655-95008656
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	POLR2A	chr1:95008440-95008903	U87	brain:	n/a	n/a
2	GTF2F1	chr1:95007247-95008830	Hela-S3	cervix:	n/a	n/a
3	MYC	chr1:95008320-95008915	MCF10A-Er-Src	breast:	n/a	chr1:95008768-95008777
4	STAT3	chr1:95008500-95008860	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:94991604-95010849	IMR90	lung:	n/a	n/a
6	POLR2A	chr1:95008543-95008884	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr1:95008585-95008955	MCF10A-Er-Src	breast:	n/a	chr1:95008770-95008777 chr1:95008769-95008777 chr1:95008769-95008777
8	STAT3	chr1:95008597-95008830	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:95000323-95009541	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr1:95008570-95008904	IMR90	lung:	n/a	chr1:95008723-95008734
11	FOS	chr1:95008484-95008958	HUVEC	blood vessel:	n/a	chr1:95008770-95008777 chr1:95008769-95008777 chr1:95008769-95008777
12	CHD1	chr1:94994939-95011321	IMR90	lung:	n/a	n/a
13	POLR2A	chr1:95008607-95008783	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr1:95008575-95009059	Hela-S3	cervix:	n/a	chr1:95008723-95008734
15	FOS	chr1:95008584-95008917	MCF10A-Er-Src	breast:	n/a	chr1:95008770-95008777 chr1:95008769-95008777 chr1:95008769-95008777
16	SPI1	chr1:95008550-95008866	HL-60	blood:	n/a	n/a
17	FOS	chr1:95008408-95008967	MCF10A-Er-Src	breast:	n/a	chr1:95008770-95008777 chr1:95008769-95008777 chr1:95008769-95008777
18	STAT3	chr1:95008583-95008951	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:95008572-95008885	Hela-S3	cervix:	n/a	n/a
20	TBP	chr1:95008031-95008941	Hela-S3	cervix:	n/a	n/a
21	RAD21	chr1:95006194-95008967	IMR90	lung:	n/a	chr1:95007044-95007058
22	FOS	chr1:95008276-95008954	MCF10A-Er-Src	breast:	n/a	chr1:95008770-95008777 chr1:95008769-95008777 chr1:95008769-95008777

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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABCD3-1	chr1:95007516-95008786	NONHSAT004594

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

Extended variants
information (count: 10 )
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];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1361600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3917615	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762485	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs841697	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs958587	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]

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	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
4	esv3437143	chr1:95006189-95008737	Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3761955	PTBP2	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95004200-95008800	Active TSS	Ovary	ovary
2	chr1:95005600-95008800	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:95006600-95008800	Active TSS	Sigmoid Colon	Sigmoid Colon
4	chr1:95006800-95009200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:95007000-95009400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:95007200-95009600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:95007400-95009400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:95007600-95008800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:95007600-95008800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr1:95007600-95008800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr1:95007600-95008800	Flanking Active TSS	Dnd41	blood
12	chr1:95007600-95008800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
13	chr1:95007600-95008800	Flanking Active TSS	Hela-S3	cervix
14	chr1:95007600-95008800	Flanking Active TSS	Osteobl	bone
15	chr1:95007600-95009000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:95007600-95009000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:95007600-95009000	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr1:95007600-95010400	Flanking Active TSS	HMEC	breast
19	chr1:95007800-95008800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:95007800-95008800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:95007800-95008800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:95007800-95008800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr1:95007800-95008800	Flanking Active TSS	NH-A	brain
24	chr1:95008000-95008800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
25	chr1:95008000-95008800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr1:95008000-95008800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
27	chr1:95008000-95008800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
28	chr1:95008000-95008800	Bivalent Enhancer	Fetal Thymus	thymus
29	chr1:95008000-95009000	Flanking Active TSS	A549	lung
30	chr1:95008000-95010600	Enhancers	HSMMtube	muscle
31	chr1:95008200-95008800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:95008200-95008800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
33	chr1:95008200-95008800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
34	chr1:95008200-95008800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:95008200-95008800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr1:95008200-95008800	Enhancers	Esophagus	oesophagus
37	chr1:95008200-95008800	Bivalent Enhancer	Fetal Brain Male	brain
38	chr1:95008200-95008800	Active TSS	Placenta	Placenta
39	chr1:95008200-95008800	Active TSS	Right Atrium	heart
40	chr1:95008200-95008800	Active TSS	Stomach Smooth Muscle	stomach
41	chr1:95008200-95009000	Enhancers	HUVEC	blood vessel
42	chr1:95008200-95009000	Flanking Active TSS	NHDF-Ad	bronchial
43	chr1:95008200-95009200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:95008200-95009600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:95008200-95009600	Weak transcription	Gastric	stomach
46	chr1:95008200-95011000	Enhancers	HSMM	muscle
47	chr1:95008200-95015600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:95008200-95015600	Weak transcription	Pancreas	Pancrea
49	chr1:95008200-95018000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:95008200-95019800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links