Variant report

Variant	rs2084490
Chromosome Location	chr2:187301264-187301265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10178888	0.87[EUR][1000 genomes]
rs10190003	0.84[ASN][1000 genomes]
rs10196955	0.84[ASN][1000 genomes]
rs10198525	0.84[ASN][1000 genomes]
rs10208643	0.84[ASN][1000 genomes]
rs1037241	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10497671	0.84[ASN][1000 genomes]
rs11675633	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11678950	0.80[EUR][1000 genomes]
rs11680486	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11688988	0.84[ASN][1000 genomes]
rs11690758	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11692028	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11692347	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11693797	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11888432	0.80[EUR][1000 genomes]
rs11895483	0.85[EUR][1000 genomes]
rs11898666	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11901465	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11903027	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12328822	0.84[ASN][1000 genomes]
rs13392819	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13393891	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13397188	0.84[ASN][1000 genomes]
rs13401304	0.80[EUR][1000 genomes]
rs13414850	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13428033	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1448848	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1448849	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16827968	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1868383	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2044683	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2084488	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2084489	0.84[ASN][1000 genomes]
rs2197139	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2370688	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2887826	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35642346	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55719959	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56137171	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61226319	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61434493	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6434167	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6709401	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6716324	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6717525	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6721789	0.84[ASN][1000 genomes]
rs6724161	0.83[EUR][1000 genomes]
rs6728382	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6731567	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6744717	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72893450	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72895449	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72897386	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72901322	0.80[EUR][1000 genomes]
rs7579259	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7584137	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7585889	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7588607	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7597954	0.84[ASN][1000 genomes]
rs7603088	0.80[EUR][1000 genomes]
rs9288129	0.84[ASN][1000 genomes]
rs9917285	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv428067	chr2:187171324-187334779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1005680	chr2:187244500-187320653	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv536080	chr2:187244500-187320653	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1001927	chr2:187264940-187325667	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv997835	chr2:187265730-187327561	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv536081	chr2:187265730-187327561	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2084490	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187290600-187304200	Weak transcription	Stomach Mucosa	stomach
2	chr2:187291800-187301800	Weak transcription	GM12878-XiMat	blood
3	chr2:187293000-187304400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:187293200-187302600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:187293800-187322000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:187294200-187301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:187295400-187302600	Weak transcription	Brain Anterior Caudate	brain
8	chr2:187295600-187302400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:187296200-187302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:187297200-187303200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:187297600-187305200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:187297800-187331200	Weak transcription	Left Ventricle	heart
13	chr2:187298000-187301800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:187298200-187304400	Weak transcription	Pancreas	Pancrea
15	chr2:187298800-187302000	Strong transcription	Fetal Intestine Large	intestine
16	chr2:187298800-187302200	Weak transcription	Esophagus	oesophagus
17	chr2:187298800-187302600	Weak transcription	Colonic Mucosa	Colon
18	chr2:187299000-187301400	Strong transcription	Primary T cells from cord blood	blood
19	chr2:187299000-187301600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr2:187299200-187301600	Strong transcription	Stomach Smooth Muscle	stomach
21	chr2:187299200-187302200	Strong transcription	HepG2	liver
22	chr2:187299400-187301400	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:187299600-187302200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr2:187299600-187319600	Weak transcription	Adipose Nuclei	Adipose
25	chr2:187299600-187322800	Weak transcription	Aorta	Aorta
26	chr2:187299800-187305200	Weak transcription	Liver	Liver
27	chr2:187299800-187305600	Weak transcription	Spleen	Spleen
28	chr2:187300000-187301600	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:187300200-187305400	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr2:187300400-187302400	Strong transcription	Primary B cells from cord blood	blood
31	chr2:187300400-187302400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:187300400-187303600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:187300600-187301400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr2:187300600-187301400	Weak transcription	Dnd41	blood
35	chr2:187300600-187301800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:187300800-187301400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:187300800-187301400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:187300800-187301400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:187300800-187302000	ZNF genes & repeats	Fetal Stomach	stomach
40	chr2:187300800-187302200	Strong transcription	Ovary	ovary
41	chr2:187300800-187302600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:187301000-187301400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:187301000-187302200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr2:187301000-187303400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr2:187301000-187303400	Weak transcription	Right Atrium	heart
46	chr2:187301200-187301400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:187301200-187301600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
48	chr2:187301200-187301600	ZNF genes & repeats	Gastric	stomach
49	chr2:187301200-187316000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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