Variant report

Variant	rs72990813
Chromosome Location	chr3:142759779-142759780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142752534..142757163-chr3:142757790..142760987,5	K562	blood:
2	chr3:142718831..142720349-chr3:142757842..142760220,2	MCF-7	breast:
3	chr3:142547621..142548188-chr3:142759314..142760110,2	K562	blood:
4	chr3:142755305..142760138-chr3:142835756..142840820,6	K562	blood:
5	chr3:142755375..142756882-chr3:142757449..142760432,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175040	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1107771	1.00[EUR][1000 genomes]
rs12107010	0.87[ASN][1000 genomes]
rs13321817	0.87[ASN][1000 genomes]
rs13322379	0.86[EUR][1000 genomes]
rs13322528	0.86[EUR][1000 genomes]
rs13325630	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16852899	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821646	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58531834	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59540153	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764683	0.86[EUR][1000 genomes]
rs6771415	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781061	0.83[ASN][1000 genomes]
rs6782124	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6797880	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805721	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806835	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72992541	0.87[ASN][1000 genomes]
rs72992555	0.86[EUR][1000 genomes]
rs7646915	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9289653	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808897	0.87[ASN][1000 genomes]
rs9808965	0.87[ASN][1000 genomes]
rs9820824	0.87[ASN][1000 genomes]
rs9839114	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842812	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868064	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871843	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876889	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877143	0.86[EUR][1000 genomes]
rs9881229	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9881390	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882184	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883936	0.87[ASN][1000 genomes]
rs9990198	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142721800-142761800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:142727400-142764400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:142728600-142769000	Weak transcription	Pancreas	Pancrea
4	chr3:142729200-142765000	Strong transcription	Dnd41	blood
5	chr3:142729200-142785200	Weak transcription	Aorta	Aorta
6	chr3:142729400-142764800	Strong transcription	K562	blood
7	chr3:142729800-142764800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:142729800-142765000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:142730200-142765000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:142730200-142765000	Strong transcription	Fetal Thymus	thymus
11	chr3:142732800-142765000	Strong transcription	HSMM	muscle
12	chr3:142733200-142764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:142734400-142785200	Weak transcription	Esophagus	oesophagus
14	chr3:142740000-142769200	Weak transcription	Gastric	stomach
15	chr3:142740200-142763200	Weak transcription	Lung	lung
16	chr3:142742400-142764800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:142742600-142764200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:142743600-142763200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:142743600-142764400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:142747000-142761800	Weak transcription	Fetal Brain Male	brain
21	chr3:142748800-142762000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:142749000-142761800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:142749000-142762000	Weak transcription	Spleen	Spleen
24	chr3:142749000-142763600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:142749000-142784200	Weak transcription	Small Intestine	intestine
26	chr3:142749200-142762000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:142749200-142763000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:142749200-142763600	Weak transcription	Psoas Muscle	Psoas
29	chr3:142749200-142765000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:142749200-142769000	Weak transcription	Right Ventricle	heart
31	chr3:142749200-142779000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:142749600-142761600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:142750400-142762000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:142751200-142762600	Weak transcription	Fetal Intestine Small	intestine
35	chr3:142751200-142763000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:142752600-142761600	Weak transcription	Fetal Brain Female	brain
37	chr3:142753400-142761400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:142753400-142762600	Weak transcription	Fetal Stomach	stomach
39	chr3:142754200-142769800	Weak transcription	Colonic Mucosa	Colon
40	chr3:142755200-142764800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:142755400-142759800	Strong transcription	NHEK	skin
42	chr3:142755400-142760000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:142755400-142764800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:142755600-142759800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr3:142755800-142759800	Strong transcription	Adipose Nuclei	Adipose
46	chr3:142755800-142761400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:142755800-142762000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:142755800-142765000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:142755800-142765000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:142755800-142765000	Strong transcription	Monocytes-CD14+_RO01746	blood

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