Variant report

Variant	rs2138898
Chromosome Location	chr1:169358811-169358812
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169346482..169351680-chr1:169353078..169360345,13	K562	blood:
2	chr1:169355278..169357561-chr1:169358415..169361333,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1018831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10429893	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465575	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465576	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489189	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732287	0.82[JPT][hapmap]
rs10800424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10800425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10800435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs10800438	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800440	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919124	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919168	0.81[ASN][1000 genomes]
rs10919174	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs1124843	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133814	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200079	0.82[JPT][hapmap]
rs12029566	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076993	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208134	0.81[ASN][1000 genomes]
rs1208135	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1208370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1208377	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1400836	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517744	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1517747	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1591733	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1856303	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1914505	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983546	0.82[JPT][hapmap]
rs2003653	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037250	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2176473	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766095	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3820059	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905328	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264046	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4656183	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656672	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427185	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6427187	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656822	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs6669901	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700375	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7415756	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533257	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7535765	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7544221	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554689	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs760603	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925892	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932301	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994986	1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2138898	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs2138898	NME7	cis	Esophagus Muscularis	GTEx
rs2138898	NME7	cis	Artery Tibial	GTEx
rs2138898	NME7	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
2	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:169338000-169365200	Weak transcription	Gastric	stomach
4	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
5	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
10	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:169340400-169366000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:169341200-169367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:169344200-169360200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:169344800-169359200	Strong transcription	HSMM	muscle
17	chr1:169344800-169361200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:169344800-169362600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:169344800-169365400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:169345000-169360800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:169345000-169366000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:169345400-169366000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:169345600-169360800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:169345600-169366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:169345800-169360800	Strong transcription	NH-A	brain
26	chr1:169345800-169365000	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:169345800-169365400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:169345800-169366000	Strong transcription	Placenta	Placenta
29	chr1:169345800-169366400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:169346600-169363400	Weak transcription	Right Ventricle	heart
31	chr1:169346600-169365400	Weak transcription	HepG2	liver
32	chr1:169346800-169360200	Weak transcription	Psoas Muscle	Psoas
33	chr1:169346800-169363800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:169347600-169362600	Strong transcription	Primary hematopoietic stem cells	blood
35	chr1:169349400-169361000	Strong transcription	Osteobl	bone
36	chr1:169349400-169361600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:169349400-169362400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:169349400-169362400	Strong transcription	Fetal Thymus	thymus
39	chr1:169349400-169363800	Strong transcription	NHEK	skin
40	chr1:169349400-169364600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:169349400-169366000	Strong transcription	Adipose Nuclei	Adipose
42	chr1:169349400-169367400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:169349600-169361000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:169349600-169362200	Strong transcription	Dnd41	blood
45	chr1:169349600-169362400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:169349800-169362200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:169350200-169366800	Weak transcription	HSMMtube	muscle
48	chr1:169350200-169368600	Weak transcription	Colonic Mucosa	Colon
49	chr1:169351000-169362600	Strong transcription	Primary T cells from cord blood	blood
50	chr1:169351400-169359200	Strong transcription	Brain Hippocampus Middle	brain

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