Variant report

Variant	rs489183
Chromosome Location	chr1:93592692-93592693
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93583706..93586639-chr1:93592635..93594148,2	K562	blood:
2	chr1:93592377..93594266-chr1:93643687..93645200,2	K562	blood:

Variant related genes	Relation type
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1010476	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038046	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2255722	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2281524	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2281525	0.87[ASN][1000 genomes]
rs2484486	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2749732	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2783490	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2783493	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2783495	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2783496	0.89[ASN][1000 genomes]
rs2783497	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2783505	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2815406	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815429	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs556446	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs579138	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61799470	0.84[AMR][1000 genomes];0.87[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 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	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
2	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
3	chr1:93548000-93601800	Weak transcription	NHLF	lung
4	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
5	chr1:93571400-93602200	Weak transcription	Colonic Mucosa	Colon
6	chr1:93572400-93599600	Weak transcription	Spleen	Spleen
7	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:93573800-93609000	Strong transcription	Fetal Thymus	thymus
9	chr1:93574200-93609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:93574600-93609000	Strong transcription	Dnd41	blood
11	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
12	chr1:93577200-93592800	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:93577200-93597000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:93577800-93601600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:93578800-93613600	Weak transcription	Psoas Muscle	Psoas
16	chr1:93578800-93620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:93579600-93595400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:93580000-93624000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:93581000-93599200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:93581200-93616800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:93582400-93599800	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:93582400-93600000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:93582400-93620400	Weak transcription	Small Intestine	intestine
25	chr1:93582400-93642800	Weak transcription	Gastric	stomach
26	chr1:93582600-93600000	Weak transcription	Ovary	ovary
27	chr1:93583000-93601400	Weak transcription	Brain Substantia Nigra	brain
28	chr1:93583000-93604200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:93583200-93595200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:93583200-93602000	Weak transcription	NHDF-Ad	bronchial
31	chr1:93583200-93628800	Weak transcription	Brain Angular Gyrus	brain
32	chr1:93583600-93592800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:93583600-93593800	Weak transcription	Fetal Stomach	stomach
34	chr1:93583600-93594400	Weak transcription	NHEK	skin
35	chr1:93583600-93595600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:93583600-93595800	Weak transcription	Brain Germinal Matrix	brain
37	chr1:93583600-93599600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:93583600-93599600	Weak transcription	Left Ventricle	heart
39	chr1:93583600-93600000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:93583600-93600800	Weak transcription	Fetal Brain Female	brain
41	chr1:93583600-93613800	Weak transcription	Lung	lung
42	chr1:93583600-93623800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
44	chr1:93584200-93600000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:93584200-93600000	Weak transcription	Osteobl	bone
46	chr1:93584400-93596200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:93584600-93594800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:93584600-93600000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:93584600-93601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:93585200-93609200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links