Variant report

Variant	rs4583974
Chromosome Location	chr6:53727489-53727490
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	chr6:53725023..53728197-chr6:53731513..53733872,3	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10948783	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10948784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193567	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12194768	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12209621	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3935664	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4128619	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4236114	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4260754	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265034	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4273680	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4331986	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4392712	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4587161	0.82[AFR][1000 genomes]
rs4612163	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4624872	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4645423	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458967	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6458968	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6904545	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6906921	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6907027	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6910777	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913431	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6935621	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6935838	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7453639	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7745548	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7749635	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7749749	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7751036	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7755924	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7761285	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9296722	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296723	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9349682	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9349683	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349684	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9367543	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9370234	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9370237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370240	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9382240	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9382242	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382245	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9382247	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9382248	0.80[ASN][1000 genomes]
rs9395879	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9395880	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9395882	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9395883	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9395884	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395887	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
4	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:53719800-53727600	Enhancers	Brain Substantia Nigra	brain
6	chr6:53719800-53727800	Enhancers	Brain Hippocampus Middle	brain
7	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
8	chr6:53720000-53727600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:53720600-53741400	Weak transcription	Dnd41	blood
10	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
11	chr6:53721600-53728000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:53723000-53728000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:53723000-53728000	Weak transcription	Pancreas	Pancrea
15	chr6:53723000-53728000	Weak transcription	Right Atrium	heart
16	chr6:53723400-53736800	Weak transcription	Stomach Mucosa	stomach
17	chr6:53725000-53727600	Enhancers	Brain Cingulate Gyrus	brain
18	chr6:53725000-53728400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:53725000-53729400	Enhancers	Brain Germinal Matrix	brain
20	chr6:53725400-53730000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr6:53725400-53730200	Enhancers	Brain Anterior Caudate	brain
22	chr6:53725400-53730400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:53725600-53728600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:53725800-53728400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:53725800-53730000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:53726000-53729000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:53726000-53729000	Enhancers	HMEC	breast
28	chr6:53726200-53729600	Enhancers	Colon Smooth Muscle	Colon
29	chr6:53726400-53727600	Enhancers	NHLF	lung
30	chr6:53726400-53729000	Enhancers	Fetal Stomach	stomach
31	chr6:53726400-53730200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:53726600-53727800	Weak transcription	HepG2	liver
33	chr6:53726600-53728200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:53726600-53728400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:53726600-53728400	Enhancers	NH-A	brain
36	chr6:53726600-53728600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr6:53726600-53729400	Enhancers	Fetal Muscle Leg	muscle
38	chr6:53726600-53730200	Enhancers	Rectal Smooth Muscle	rectum
39	chr6:53726600-53730400	Enhancers	Fetal Brain Male	brain
40	chr6:53726800-53728400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:53726800-53728600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr6:53726800-53729800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:53727000-53728800	Weak transcription	Fetal Intestine Small	intestine
44	chr6:53727000-53729200	Enhancers	Fetal Lung	lung
45	chr6:53727200-53727600	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr6:53727200-53727600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr6:53727200-53728200	Enhancers	Osteobl	bone
48	chr6:53727200-53729000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr6:53727200-53729400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:53727200-53729400	Enhancers	Fetal Brain Female	brain

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