Variant report

Variant	rs2138873
Chromosome Location	chr2:172714067-172714068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10188587	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10191399	0.91[AFR][1000 genomes]
rs10196521	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1022358	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10432474	0.80[AFR][1000 genomes]
rs10439296	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10930496	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930498	0.83[AMR][1000 genomes]
rs10930500	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1105264	0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11692418	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11903123	0.85[AFR][1000 genomes]
rs12468218	0.82[AMR][1000 genomes]
rs12478215	0.85[AMR][1000 genomes]
rs12617265	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12619137	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692971	0.82[AFR][1000 genomes]
rs12692977	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692979	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13017988	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13018515	0.80[AMR][1000 genomes]
rs13021571	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1400816	0.86[AFR][1000 genomes]
rs1443700	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1878583	0.90[AFR][1000 genomes]
rs1996425	0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2056202	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176466	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357064	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2357206	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2884123	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770443	0.84[ASN][1000 genomes]
rs3770444	0.93[AFR][1000 genomes]
rs3770453	0.80[EUR][1000 genomes]
rs3770457	0.81[AFR][1000 genomes]
rs3821094	0.83[AFR][1000 genomes]
rs3821096	0.84[AFR][1000 genomes]
rs4072279	0.82[AMR][1000 genomes]
rs4324292	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4668413	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668415	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668416	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668417	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4668419	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59414074	0.89[ASN][1000 genomes]
rs59853867	0.82[AMR][1000 genomes]
rs6433313	0.81[AFR][1000 genomes]
rs6433315	0.86[AFR][1000 genomes]
rs6433316	0.81[AFR][1000 genomes]
rs6433317	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6708365	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6709299	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6711813	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6726991	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6727459	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736159	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6740705	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6757680	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6758494	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6760680	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7340516	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7371503	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7580132	0.85[AMR][1000 genomes]
rs7580232	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583860	0.86[AFR][1000 genomes]
rs7588025	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7594478	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7604933	0.85[AFR][1000 genomes]
rs925881	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9636293	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs970948	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv583611	chr2:172683481-172750257	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv1006214	chr2:172691689-172754296	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv536036	chr2:172691689-172754296	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2138873	AC068039.4	cis	Stomach	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172690200-172720600	Weak transcription	Gastric	stomach
2	chr2:172690200-172721000	Weak transcription	Aorta	Aorta
3	chr2:172690200-172750200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:172691400-172738600	Weak transcription	Esophagus	oesophagus
5	chr2:172692200-172714400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:172692200-172733400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:172693200-172728000	Weak transcription	Colonic Mucosa	Colon
8	chr2:172693400-172734800	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:172693600-172724200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:172693600-172734400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:172693600-172734600	Weak transcription	HSMM	muscle
12	chr2:172693800-172715000	Weak transcription	NHLF	lung
13	chr2:172693800-172719000	Weak transcription	Psoas Muscle	Psoas
14	chr2:172693800-172720600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:172693800-172721000	Weak transcription	Brain Anterior Caudate	brain
16	chr2:172693800-172721000	Weak transcription	Spleen	Spleen
17	chr2:172693800-172725800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:172693800-172727000	Weak transcription	Fetal Kidney	kidney
19	chr2:172693800-172732600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:172693800-172734600	Weak transcription	Right Ventricle	heart
21	chr2:172694000-172724200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:172694000-172724200	Weak transcription	Brain Germinal Matrix	brain
23	chr2:172694000-172732800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:172694000-172734600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:172694000-172734600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:172694600-172720800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:172694800-172714600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:172698600-172724200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:172698600-172734600	Weak transcription	Adipose Nuclei	Adipose
30	chr2:172699000-172734600	Weak transcription	Brain Angular Gyrus	brain
31	chr2:172699200-172714400	Weak transcription	Fetal Lung	lung
32	chr2:172699400-172721000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:172699600-172731400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:172700200-172724200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:172700200-172724400	Weak transcription	Fetal Stomach	stomach
36	chr2:172700400-172724200	Weak transcription	Fetal Brain Female	brain
37	chr2:172704200-172724200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:172704800-172731000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:172705000-172719000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:172705200-172731400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:172705400-172735200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:172709400-172734400	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:172709600-172720400	Weak transcription	Fetal Heart	heart
44	chr2:172709600-172749600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:172709600-172749600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:172709800-172714600	Weak transcription	NHDF-Ad	bronchial
47	chr2:172709800-172731400	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:172710000-172724200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:172710400-172723800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:172710600-172724200	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links