Variant report

Variant	rs2084489
Chromosome Location	chr2:187301080-187301081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10169008	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10169206	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177153	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10190003	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196955	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198525	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200749	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205170	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10208643	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497671	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931240	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11675633	0.89[ASN][1000 genomes]
rs11688988	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690758	0.89[ASN][1000 genomes]
rs11692347	0.89[ASN][1000 genomes]
rs11888880	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11888881	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11901465	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11903027	0.89[ASN][1000 genomes]
rs12328822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392819	0.89[ASN][1000 genomes]
rs13397188	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398352	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13414850	0.89[ASN][1000 genomes]
rs13428033	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1448848	0.89[ASN][1000 genomes]
rs1448855	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1448857	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1868383	0.89[ASN][1000 genomes]
rs2084488	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2084490	0.84[ASN][1000 genomes]
rs2197139	0.89[ASN][1000 genomes]
rs2370688	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2887826	0.89[ASN][1000 genomes]
rs34234405	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35642346	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56137171	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61434493	0.89[ASN][1000 genomes]
rs6434174	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710436	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6715493	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717505	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6721789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728382	0.89[ASN][1000 genomes]
rs6728400	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6744717	0.89[ASN][1000 genomes]
rs72895449	0.89[ASN][1000 genomes]
rs7579259	0.89[ASN][1000 genomes]
rs7582412	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7584137	0.89[ASN][1000 genomes]
rs7585905	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597954	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606920	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9288129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917285	0.89[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
rs2084489	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187288600-187301200	Weak transcription	Gastric	stomach
2	chr2:187290600-187304200	Weak transcription	Stomach Mucosa	stomach
3	chr2:187291800-187301800	Weak transcription	GM12878-XiMat	blood
4	chr2:187292000-187301200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:187293000-187304400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr2:187293200-187302600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:187293800-187322000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:187294200-187301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:187295400-187302600	Weak transcription	Brain Anterior Caudate	brain
10	chr2:187295600-187302400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:187296200-187302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:187297200-187303200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:187297600-187305200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:187297800-187331200	Weak transcription	Left Ventricle	heart
15	chr2:187298000-187301800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:187298200-187301200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:187298200-187304400	Weak transcription	Pancreas	Pancrea
18	chr2:187298800-187302000	Strong transcription	Fetal Intestine Large	intestine
19	chr2:187298800-187302200	Weak transcription	Esophagus	oesophagus
20	chr2:187298800-187302600	Weak transcription	Colonic Mucosa	Colon
21	chr2:187299000-187301400	Strong transcription	Primary T cells from cord blood	blood
22	chr2:187299000-187301600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:187299200-187301600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr2:187299200-187302200	Strong transcription	HepG2	liver
25	chr2:187299400-187301200	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:187299400-187301400	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:187299600-187302200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:187299600-187319600	Weak transcription	Adipose Nuclei	Adipose
29	chr2:187299600-187322800	Weak transcription	Aorta	Aorta
30	chr2:187299800-187305200	Weak transcription	Liver	Liver
31	chr2:187299800-187305600	Weak transcription	Spleen	Spleen
32	chr2:187300000-187301600	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:187300200-187305400	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr2:187300400-187301200	Strong transcription	Primary hematopoietic stem cells	blood
35	chr2:187300400-187302400	Strong transcription	Primary B cells from cord blood	blood
36	chr2:187300400-187302400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:187300400-187303600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:187300600-187301400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr2:187300600-187301400	Weak transcription	Dnd41	blood
40	chr2:187300600-187301800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:187300800-187301400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:187300800-187301400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:187300800-187301400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:187300800-187302000	ZNF genes & repeats	Fetal Stomach	stomach
45	chr2:187300800-187302200	Strong transcription	Ovary	ovary
46	chr2:187300800-187302600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:187301000-187301400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:187301000-187302200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr2:187301000-187303400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:187301000-187303400	Weak transcription	Right Atrium	heart

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