Variant report

Variant	rs17023837
Chromosome Location	chr2:39681558-39681559
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-1	chr2:39681438-39681867	ENSG00000231312.2

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10153665	0.87[EUR][1000 genomes]
rs10170424	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10170617	0.94[EUR][1000 genomes]
rs10172736	0.83[EUR][1000 genomes]
rs10173556	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10175038	0.83[EUR][1000 genomes]
rs10195629	0.84[EUR][1000 genomes]
rs1035232	0.91[EUR][1000 genomes]
rs10865149	0.89[EUR][1000 genomes]
rs10865150	0.87[EUR][1000 genomes]
rs10865152	0.85[EUR][1000 genomes]
rs11124668	0.83[EUR][1000 genomes]
rs11124673	0.84[EUR][1000 genomes]
rs11124676	0.82[EUR][1000 genomes]
rs11124679	0.89[EUR][1000 genomes]
rs1125839	0.87[EUR][1000 genomes]
rs11688728	0.91[EUR][1000 genomes]
rs1211996	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12622941	0.84[EUR][1000 genomes]
rs1468902	0.84[EUR][1000 genomes]
rs17023874	1.00[AFR][1000 genomes]
rs1861735	0.87[EUR][1000 genomes]
rs1922827	0.82[EUR][1000 genomes]
rs2005892	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2178762	0.89[EUR][1000 genomes]
rs2193422	0.83[EUR][1000 genomes]
rs2373534	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2373535	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2542008	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2888594	0.85[EUR][1000 genomes]
rs2888598	0.89[EUR][1000 genomes]
rs3755177	0.87[EUR][1000 genomes]
rs3755178	0.85[EUR][1000 genomes]
rs3770670	0.87[EUR][1000 genomes]
rs3770675	0.85[EUR][1000 genomes]
rs3770678	0.83[EUR][1000 genomes]
rs6544213	0.83[EUR][1000 genomes]
rs6544220	0.82[EUR][1000 genomes]
rs6544222	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6544224	0.91[EUR][1000 genomes]
rs6712274	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6712921	0.85[EUR][1000 genomes]
rs6718134	0.85[EUR][1000 genomes]
rs6725938	0.83[EUR][1000 genomes]
rs6732611	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6736700	0.85[EUR][1000 genomes]
rs6741019	0.83[EUR][1000 genomes]
rs6742170	0.91[EUR][1000 genomes]
rs6743041	0.84[EUR][1000 genomes]
rs6753323	0.91[EUR][1000 genomes]
rs6756183	0.87[EUR][1000 genomes]
rs6760382	0.85[EUR][1000 genomes]
rs7578136	0.83[EUR][1000 genomes]
rs7579414	0.85[EUR][1000 genomes]
rs759589	0.89[EUR][1000 genomes]
rs7600014	0.87[EUR][1000 genomes]
rs7600046	0.87[EUR][1000 genomes]
rs7601700	0.87[EUR][1000 genomes]
rs7603337	0.89[EUR][1000 genomes]
rs7604047	0.81[EUR][1000 genomes]
rs7608153	0.83[EUR][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	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv215442	chr2:39676634-39681883	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17023837	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39665200-39696000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39665600-39681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:39665600-39684200	Weak transcription	Lung	lung
4	chr2:39665600-39685600	Weak transcription	Left Ventricle	heart
5	chr2:39665600-39694600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:39665600-39694800	Weak transcription	Pancreas	Pancrea
7	chr2:39666200-39696600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:39666600-39682200	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:39666800-39681600	Weak transcription	Ovary	ovary
10	chr2:39667000-39681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:39667000-39694600	Weak transcription	HSMMtube	muscle
12	chr2:39667200-39685200	Weak transcription	NHEK	skin
13	chr2:39667200-39694600	Weak transcription	NHLF	lung
14	chr2:39667200-39694800	Weak transcription	Brain Angular Gyrus	brain
15	chr2:39667200-39696400	Weak transcription	Fetal Heart	heart
16	chr2:39667400-39682000	Weak transcription	HSMM	muscle
17	chr2:39667400-39694600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:39667400-39694600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:39668200-39684800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:39668200-39685000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:39668200-39694800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:39668200-39696800	Weak transcription	Right Ventricle	heart
23	chr2:39670400-39682800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:39670400-39685000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:39670800-39684800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:39671000-39682200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:39671200-39685000	Weak transcription	Aorta	Aorta
28	chr2:39671600-39682600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:39671800-39682000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:39672200-39684600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:39675000-39696400	Weak transcription	Fetal Kidney	kidney
32	chr2:39675200-39682600	Weak transcription	Osteobl	bone
33	chr2:39675200-39682800	Weak transcription	HMEC	breast
34	chr2:39675200-39686000	Weak transcription	NHDF-Ad	bronchial
35	chr2:39675400-39682200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:39675400-39694600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:39675600-39682400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:39676000-39684800	Weak transcription	Fetal Intestine Small	intestine
39	chr2:39677200-39687400	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:39678000-39696800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:39678200-39694600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:39678800-39682000	Weak transcription	HepG2	liver
43	chr2:39679600-39682000	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:39680400-39682200	Enhancers	Fetal Lung	lung
45	chr2:39680800-39682000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:39680800-39683800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:39680800-39684200	Weak transcription	Primary T cells from cord blood	blood
48	chr2:39680800-39684800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:39681000-39682400	Strong transcription	Liver	Liver
50	chr2:39681000-39683400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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