Variant report

Variant	rs2275162
Chromosome Location	chr1:241677035-241677036
allele	A/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	GATA3	chr1:241676876-241677048	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:241676840..241679427-chr1:241681305..241683481,5	MCF-7	breast:

Variant related genes	Relation type
FH	TF binding region
ENSG00000091483	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs16841808	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3765803	0.83[ASN][1000 genomes]
rs56957678	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58766151	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59580206	0.88[ASN][1000 genomes]
rs59625977	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60043538	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60673334	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61543265	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61737760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66497254	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66626588	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66669018	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6678986	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6679186	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66799800	0.91[ASN][1000 genomes]
rs6690411	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67219057	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67267325	0.86[EUR][1000 genomes]
rs67439618	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67528386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67794990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67802946	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68119865	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72766004	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73135296	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241655800-241677200	Strong transcription	Liver	Liver
2	chr1:241656800-241678200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:241657000-241677200	Strong transcription	Adipose Nuclei	Adipose
4	chr1:241657000-241677400	Strong transcription	Fetal Thymus	thymus
5	chr1:241657000-241680000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:241657200-241677200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:241657200-241677400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr1:241657400-241678600	Strong transcription	Dnd41	blood
9	chr1:241657400-241680000	Strong transcription	Primary B cells from cord blood	blood
10	chr1:241659000-241682000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:241659200-241679800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:241659600-241679000	Strong transcription	HMEC	breast
13	chr1:241661200-241681400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:241664000-241677200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:241664800-241680600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:241665000-241677400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:241665000-241677400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:241665000-241679200	Strong transcription	Hela-S3	cervix
19	chr1:241665000-241679600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:241667400-241680800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:241667400-241681800	Weak transcription	Fetal Brain Male	brain
22	chr1:241667600-241681800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:241667800-241682000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:241668000-241679600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:241668000-241680600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:241668000-241682000	Weak transcription	Pancreas	Pancrea
27	chr1:241668000-241682200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:241668000-241682200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:241668000-241682200	Weak transcription	Esophagus	oesophagus
30	chr1:241668600-241678400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:241668600-241678400	Weak transcription	Fetal Intestine Small	intestine
32	chr1:241668800-241680400	Weak transcription	Fetal Stomach	stomach
33	chr1:241669800-241677800	Strong transcription	NHEK	skin
34	chr1:241670000-241679800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:241671600-241679200	Strong transcription	Osteobl	bone
36	chr1:241671600-241679800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:241671800-241679800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:241671800-241679800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:241671800-241682000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:241672000-241681200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:241672000-241681200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:241672000-241681200	Weak transcription	Stomach Mucosa	stomach
43	chr1:241672000-241681400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:241672000-241682000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:241672200-241681800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:241672400-241679400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:241672800-241681200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:241673000-241677200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:241673200-241678200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:241673200-241679000	Strong transcription	NHDF-Ad	bronchial

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