Variant report

Variant	rs2114592
Chromosome Location	chr2:231075206-231075207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10168052	0.95[ASN][1000 genomes]
rs10177277	0.95[ASN][1000 genomes]
rs10755048	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10755049	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10755050	0.93[ASN][1000 genomes]
rs10804364	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10933328	0.93[ASN][1000 genomes]
rs1124534	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11556887	0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs12474611	0.85[ASN][1000 genomes]
rs12474616	0.96[ASN][1000 genomes]
rs12474683	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12615975	0.80[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12616762	0.93[ASN][1000 genomes]
rs12618921	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12619729	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12619732	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1469345	0.95[ASN][1000 genomes]
rs1896258	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1896259	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1978582	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1978583	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1985603	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081714	0.96[ASN][1000 genomes]
rs2396709	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2396711	0.93[ASN][1000 genomes]
rs3769837	0.96[ASN][1000 genomes]
rs3769839	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41309108	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41345344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41423848	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4327229	0.93[ASN][1000 genomes]
rs4327230	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4972942	0.96[ASN][1000 genomes]
rs4973285	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4973286	0.93[ASN][1000 genomes]
rs4973287	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4973288	0.93[ASN][1000 genomes]
rs4973289	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4973290	0.95[ASN][1000 genomes]
rs4973291	0.93[ASN][1000 genomes]
rs4973292	0.96[ASN][1000 genomes]
rs4973293	0.96[ASN][1000 genomes]
rs4973294	0.93[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs4973296	0.92[ASN][1000 genomes]
rs4973297	0.96[ASN][1000 genomes]
rs4973298	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs55809057	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55945652	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55956818	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56159955	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56275915	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56301614	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56412815	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59536070	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61182521	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6436919	0.83[ASN][1000 genomes]
rs6735604	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs6743028	0.96[ASN][1000 genomes]
rs67469122	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750748	0.96[ASN][1000 genomes]
rs6752361	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6755998	0.82[ASN][1000 genomes]
rs72982403	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982411	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982413	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72982416	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982421	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982424	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73000348	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73000367	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73000371	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561924	0.96[ASN][1000 genomes]
rs7583769	0.96[ASN][1000 genomes]
rs7592927	0.96[ASN][1000 genomes]
rs7603350	0.96[ASN][1000 genomes]
rs9061	0.86[EUR][1000 genomes]
rs930031	0.94[ASN][1000 genomes]
rs930032	0.94[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs958978	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[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	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking 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	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2114592	SNORA75	cis	cerebellum	SCAN
rs2114592	ALPI	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231035400-231077000	Weak transcription	HepG2	liver
2	chr2:231059000-231082800	Weak transcription	Stomach Mucosa	stomach
3	chr2:231062200-231081600	Strong transcription	Liver	Liver
4	chr2:231062400-231081600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:231062600-231079200	Strong transcription	Stomach Smooth Muscle	stomach
6	chr2:231062600-231080600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:231062600-231081400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:231062600-231081400	Strong transcription	Adipose Nuclei	Adipose
9	chr2:231062600-231081400	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:231062600-231081400	Strong transcription	Fetal Thymus	thymus
11	chr2:231062600-231081600	Strong transcription	Fetal Lung	lung
12	chr2:231062600-231081600	Strong transcription	Placenta	Placenta
13	chr2:231062600-231081600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr2:231062600-231081600	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:231062600-231081800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr2:231062600-231082200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:231062600-231082400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:231062600-231084200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:231062800-231080600	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr2:231062800-231081000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:231063000-231077000	Weak transcription	Psoas Muscle	Psoas
22	chr2:231063000-231080200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:231063000-231084000	Weak transcription	Hela-S3	cervix
24	chr2:231063200-231075800	Weak transcription	Colonic Mucosa	Colon
25	chr2:231063200-231081200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:231063200-231084000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:231063400-231082200	Strong transcription	Fetal Muscle Leg	muscle
28	chr2:231064800-231084000	Weak transcription	Fetal Heart	heart
29	chr2:231065000-231081000	Strong transcription	Fetal Intestine Large	intestine
30	chr2:231065000-231081400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:231066200-231083200	Weak transcription	HUVEC	blood vessel
32	chr2:231066200-231084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:231066400-231081600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:231067000-231076600	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr2:231067000-231077400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:231067000-231077400	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr2:231067000-231081400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr2:231067200-231079000	Strong transcription	Brain Hippocampus Middle	brain
39	chr2:231067200-231081600	Strong transcription	Left Ventricle	heart
40	chr2:231067400-231077400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:231067600-231084200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr2:231067800-231077400	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr2:231068200-231082200	Strong transcription	Ovary	ovary
44	chr2:231068200-231084400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:231068400-231081800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:231068400-231084000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:231069400-231079200	Strong transcription	Brain Substantia Nigra	brain
48	chr2:231069400-231081600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:231069600-231076000	Genic enhancers	Primary monocytes fromperipheralblood	blood
50	chr2:231069800-231077600	Strong transcription	HSMM	muscle

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