Variant report

Variant	rs2283873
Chromosome Location	chr22:31013296-31013297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11913239	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433541	0.80[ASN][1000 genomes]
rs16988855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16988936	0.82[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs2009857	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2072195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2267162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2267165	0.94[ASN][1000 genomes]
rs2267166	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs5994329	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs5997722	0.84[JPT][hapmap]
rs72558391	0.88[ASN][1000 genomes]
rs7288385	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7288627	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7289549	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7290898	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73396379	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73396395	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73398305	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8135379	0.80[ASN][1000 genomes]
rs8141515	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9306264	0.80[ASN][1000 genomes]
rs9606762	0.81[JPT][hapmap]
rs9621051	0.80[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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Wilms tumor	22544364	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2283873	TCN2	cis	lymphoblastoid	seeQTL
rs2283873	DUSP18	cis	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31003200-31031200	Weak transcription	Aorta	Aorta
2	chr22:31003800-31030600	Weak transcription	Thymus	Thymus
3	chr22:31004200-31013400	Weak transcription	Pancreas	Pancrea
4	chr22:31004400-31020200	Weak transcription	Fetal Kidney	kidney
5	chr22:31005000-31022200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr22:31006000-31019200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr22:31006000-31020800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr22:31006000-31023200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:31006000-31023200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr22:31006000-31030400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr22:31006000-31030600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr22:31006000-31030600	Weak transcription	Colonic Mucosa	Colon
13	chr22:31006200-31017400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr22:31006200-31017400	Strong transcription	Fetal Stomach	stomach
15	chr22:31006200-31019400	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr22:31006200-31023800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr22:31006200-31030600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr22:31006400-31013600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr22:31006400-31015000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr22:31006400-31017000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr22:31006400-31023000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr22:31006400-31023200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:31006400-31023400	Strong transcription	Fetal Intestine Small	intestine
24	chr22:31006600-31017000	Strong transcription	Brain Germinal Matrix	brain
25	chr22:31006600-31020000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr22:31006600-31030400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr22:31006800-31030200	Weak transcription	Placenta	Placenta
28	chr22:31007000-31017200	Strong transcription	Liver	Liver
29	chr22:31007000-31030600	Weak transcription	Fetal Brain Male	brain
30	chr22:31007200-31019200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr22:31007600-31030200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr22:31008000-31030400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:31008400-31023200	Strong transcription	Adipose Nuclei	Adipose
34	chr22:31008600-31014000	Strong transcription	Brain Substantia Nigra	brain
35	chr22:31008800-31013800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr22:31008800-31019000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr22:31009600-31017000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr22:31009800-31015800	Strong transcription	Fetal Lung	lung
39	chr22:31010200-31022400	Weak transcription	HUVEC	blood vessel
40	chr22:31011200-31019600	Strong transcription	Fetal Muscle Leg	muscle
41	chr22:31011600-31017200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr22:31011600-31024400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr22:31011600-31026000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr22:31011800-31019200	Strong transcription	Spleen	Spleen
45	chr22:31011800-31030200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr22:31011800-31030600	Weak transcription	Right Ventricle	heart
47	chr22:31012000-31013400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr22:31012000-31013400	Weak transcription	Brain Hippocampus Middle	brain
49	chr22:31012000-31013600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr22:31012000-31018200	Weak transcription	Brain Cingulate Gyrus	brain

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