Variant report

Variant	rs2029858
Chromosome Location	chr1:62107806-62107807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:61681397..61683015-chr1:62107574..62109680,2	MCF-7	breast:
2	chr1:62106350..62108369-chr1:62114638..62116326,2	K562	blood:
3	chr1:61519880..61523708-chr1:62105298..62109732,4	MCF-7	breast:
4	chr1:62107692..62111975-chr1:62207507..62210400,5	MCF-7	breast:
5	chr1:61961790..61962305-chr1:62107717..62108447,2	MCF-7	breast:
6	chr1:62107133..62108121-chr1:62124846..62125524,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132849	Chromatin interaction
ENSG00000271200	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10736397	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10736398	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10889245	0.81[EUR][1000 genomes]
rs11207794	0.82[EUR][1000 genomes]
rs12567173	0.82[EUR][1000 genomes]
rs1933295	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6668107	0.80[EUR][1000 genomes]
rs6686620	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1007318	chr1:62083960-62113102	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv1831777	chr1:62086216-62119201	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv508226	chr1:62091093-62140604	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv546377	chr1:62103021-62116913	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2029858	USP1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62103400-62108000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:62103400-62146400	Weak transcription	Gastric	stomach
3	chr1:62103800-62108000	Enhancers	Fetal Stomach	stomach
4	chr1:62103800-62108000	Enhancers	Rectal Smooth Muscle	rectum
5	chr1:62104400-62108400	Enhancers	Fetal Muscle Leg	muscle
6	chr1:62105200-62109800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:62105400-62108200	Weak transcription	Esophagus	oesophagus
8	chr1:62106800-62108000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:62106800-62108000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:62106800-62108000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:62106800-62108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:62106800-62108400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:62106800-62108600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:62106800-62108600	Enhancers	Fetal Thymus	thymus
15	chr1:62107000-62108600	Enhancers	Fetal Brain Male	brain
16	chr1:62107200-62108000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:62107200-62108000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr1:62107200-62108000	Bivalent Enhancer	HepG2	liver
19	chr1:62107200-62108600	Enhancers	Stomach Mucosa	stomach
20	chr1:62107400-62108200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:62107400-62108200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:62107400-62108200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:62107400-62108400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr1:62107400-62108600	Weak transcription	Aorta	Aorta
25	chr1:62107400-62109200	Weak transcription	Brain Germinal Matrix	brain
26	chr1:62107400-62109200	Enhancers	Placenta	Placenta
27	chr1:62107600-62108000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr1:62107600-62108000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:62107600-62108000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:62107600-62108000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:62107600-62108000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr1:62107600-62108000	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr1:62107600-62108000	Enhancers	HUVEC	blood vessel
34	chr1:62107600-62108000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr1:62107600-62108200	Enhancers	Adipose Nuclei	Adipose
36	chr1:62107600-62108400	Enhancers	Right Atrium	heart
37	chr1:62107600-62108600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr1:62107600-62108600	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr1:62107600-62108600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:62107600-62108600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:62107600-62108800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:62107800-62108000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr1:62107800-62108000	Enhancers	Colonic Mucosa	Colon
44	chr1:62107800-62108000	Enhancers	Fetal Brain Female	brain
45	chr1:62107800-62108000	Enhancers	Ovary	ovary
46	chr1:62107800-62108000	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr1:62107800-62108200	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr1:62107800-62108200	Enhancers	Brain Cingulate Gyrus	brain
49	chr1:62107800-62108400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:62107800-62108400	Enhancers	Colon Smooth Muscle	Colon

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