Variant report

Variant	rs3890776
Chromosome Location	chr5:112434746-112434747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112433359..112435186-chr5:112441396..112444395,2	K562	blood:
2	chr5:112428968..112430788-chr5:112433593..112437336,4	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10045658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10053994	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10058407	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10063834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10067901	0.83[EUR][1000 genomes]
rs10078431	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10223151	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10223152	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10477486	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10478102	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10478106	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11241190	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11743369	0.83[EUR][1000 genomes]
rs11744218	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11744817	0.81[ASN][1000 genomes]
rs11744828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11744956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11750093	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11960706	0.99[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12513669	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13173830	0.88[EUR][1000 genomes]
rs13174818	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227947	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2227950	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28535973	0.80[ASN][1000 genomes]
rs28645351	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28774401	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36182962	0.93[ASN][1000 genomes]
rs3890775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235788	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4283779	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4397121	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4463174	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4645326	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705539	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56054154	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6594672	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6594673	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6594675	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6594679	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6859813	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6859911	0.86[AMR][1000 genomes]
rs6861166	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6862481	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6863319	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6865444	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6865585	0.81[ASN][1000 genomes]
rs6866442	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6866566	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6866706	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6866718	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6869383	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6869399	0.83[EUR][1000 genomes]
rs6873623	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6874220	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6874314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6874595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6874727	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6878846	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6879138	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6879633	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879634	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6879942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6882689	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6894700	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6898297	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7708475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7714010	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714160	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714275	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714334	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714349	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714363	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7714492	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7724258	0.83[AMR][1000 genomes]
rs7728858	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7728921	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7732048	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7734411	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7734511	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7736823	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7737329	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9326874	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9326875	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112391600-112439000	Weak transcription	Gastric	stomach
3	chr5:112399800-112441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:112404400-112436800	Weak transcription	Fetal Brain Male	brain
5	chr5:112411200-112443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:112412000-112435200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:112417800-112436800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:112418400-112441600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:112418600-112436600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:112418600-112441400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:112419600-112436600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:112420800-112436800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:112421000-112437000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:112421000-112439000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:112421400-112437200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:112424200-112435600	Weak transcription	Small Intestine	intestine
17	chr5:112424400-112448000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:112426000-112435200	Weak transcription	Adipose Nuclei	Adipose
19	chr5:112426000-112441600	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:112426200-112437400	Weak transcription	Aorta	Aorta
21	chr5:112426200-112445000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:112426600-112435600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:112426600-112453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:112426800-112435400	Weak transcription	Fetal Lung	lung
25	chr5:112426800-112450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
27	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
29	chr5:112427000-112440800	Weak transcription	NH-A	brain
30	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
31	chr5:112427200-112448200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr5:112427600-112435600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:112427600-112441600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:112427600-112442000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:112427600-112443200	Weak transcription	Brain Substantia Nigra	brain
36	chr5:112428000-112440200	Strong transcription	Liver	Liver
37	chr5:112428400-112440200	Strong transcription	Fetal Stomach	stomach
38	chr5:112428600-112445000	Weak transcription	Placenta	Placenta
39	chr5:112429200-112435400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:112429800-112437400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:112430400-112441000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:112431000-112435200	Weak transcription	NHDF-Ad	bronchial
43	chr5:112431000-112436800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr5:112431000-112439000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:112431000-112440000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:112431000-112442600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr5:112431600-112435400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:112431600-112440200	Strong transcription	Ovary	ovary
50	chr5:112432200-112434800	Strong transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links