Variant report

Variant	rs12410387
Chromosome Location	chr1:169205870-169205871
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1018832	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10458388	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10458394	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10489190	1.00[AFR][1000 genomes]
rs10489417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494477	1.00[AFR][1000 genomes]
rs10494478	1.00[AFR][1000 genomes]
rs10800433	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10919074	0.83[AMR][1000 genomes]
rs10919085	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919087	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10919093	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10919114	0.86[ASN][1000 genomes]
rs10919122	1.00[AFR][1000 genomes]
rs10919123	1.00[AFR][1000 genomes]
rs10919125	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10919127	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10919128	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10919147	1.00[AFR][1000 genomes]
rs10919149	1.00[AFR][1000 genomes]
rs10919150	1.00[AFR][1000 genomes]
rs10919153	1.00[AFR][1000 genomes]
rs10919158	1.00[AFR][1000 genomes]
rs10919162	1.00[AFR][1000 genomes]
rs10919165	1.00[AFR][1000 genomes]
rs12021696	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022617	1.00[AFR][1000 genomes]
rs12022768	1.00[AFR][1000 genomes]
rs12025397	1.00[AFR][1000 genomes]
rs12025566	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12025721	1.00[AFR][1000 genomes]
rs12028197	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028208	1.00[AFR][1000 genomes]
rs12029800	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12029857	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12030541	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12030810	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12031371	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12035622	0.83[AMR][1000 genomes]
rs12036426	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12037926	1.00[AFR][1000 genomes]
rs12042082	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12042990	1.00[AFR][1000 genomes]
rs12044982	1.00[AFR][1000 genomes]
rs12045803	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12048188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401962	1.00[AFR][1000 genomes]
rs12401966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402774	1.00[AFR][1000 genomes]
rs12403181	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405185	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12405725	1.00[AFR][1000 genomes]
rs12406341	0.83[AMR][1000 genomes]
rs12408636	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410241	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410548	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12567342	1.00[AFR][1000 genomes]
rs1517742	1.00[AFR][1000 genomes]
rs1517746	1.00[AFR][1000 genomes]
rs17345156	0.83[AMR][1000 genomes]
rs17345426	1.00[AFR][1000 genomes]
rs17345531	1.00[AFR][1000 genomes]
rs17349677	1.00[AFR][1000 genomes]
rs17518147	1.00[AFR][1000 genomes]
rs17576927	1.00[AFR][1000 genomes]
rs2000321	0.80[AMR][1000 genomes]
rs2001155	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34323371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766074	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3766101	1.00[AFR][1000 genomes]
rs4497270	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4562680	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72704035	1.00[AFR][1000 genomes]
rs72706963	0.80[AMR][1000 genomes]
rs72706975	0.83[AMR][1000 genomes]
rs7528142	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7556463	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	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
4	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1834321	chr1:169180302-169240975	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv1845262	chr1:169180302-169240975	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription 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
8	nsv525520	chr1:169191860-169240084	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1845267	chr1:169191860-169240975	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1849515	chr1:169191860-169240975	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	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
12	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1000254	chr1:169203554-169271792	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12410387	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169172400-169207600	Weak transcription	Esophagus	oesophagus
2	chr1:169172600-169227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:169176600-169206200	Weak transcription	Aorta	Aorta
4	chr1:169177400-169207400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:169180000-169210000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:169180600-169206200	Weak transcription	Left Ventricle	heart
7	chr1:169184400-169206200	Weak transcription	Lung	lung
8	chr1:169184800-169207400	Weak transcription	Ovary	ovary
9	chr1:169187600-169207800	Weak transcription	Primary T cells from cord blood	blood
10	chr1:169187800-169211800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:169192200-169209600	Weak transcription	NHEK	skin
12	chr1:169192400-169210000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:169194000-169210000	Weak transcription	NHDF-Ad	bronchial
14	chr1:169194800-169207400	Weak transcription	Primary B cells from cord blood	blood
15	chr1:169194800-169214000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:169195200-169207600	Weak transcription	Fetal Lung	lung
17	chr1:169195400-169207600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:169197200-169206200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:169197200-169207600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:169197200-169210200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:169197600-169210200	Weak transcription	Brain Substantia Nigra	brain
22	chr1:169198000-169209800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:169199200-169210200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:169199200-169211600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:169199600-169209800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:169201000-169207800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:169201000-169212800	Weak transcription	Psoas Muscle	Psoas
28	chr1:169202400-169208800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:169203600-169206800	Enhancers	Liver	Liver
30	chr1:169204600-169206200	Enhancers	Rectal Smooth Muscle	rectum
31	chr1:169205000-169206400	Enhancers	Colon Smooth Muscle	Colon
32	chr1:169205200-169209800	Weak transcription	HUVEC	blood vessel
33	chr1:169205400-169206400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:169205600-169207600	Weak transcription	Fetal Heart	heart
35	chr1:169205600-169207600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:169205800-169207800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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