Variant report

Variant	rs12144230
Chromosome Location	chr1:169191468-169191469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10800413	0.81[EUR][1000 genomes]
rs10800418	0.81[EUR][1000 genomes]
rs10919075	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10919099	0.81[EUR][1000 genomes]
rs10919101	0.81[EUR][1000 genomes]
rs11810319	0.81[EUR][1000 genomes]
rs12080100	0.81[EUR][1000 genomes]
rs12084793	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12116551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12117362	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12117559	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12120007	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12120960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12122348	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12124738	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12125057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12130858	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12140995	0.81[EUR][1000 genomes]
rs12143790	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12143963	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12144832	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12145193	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12145897	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12728614	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12730917	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12730920	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12736817	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12740501	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12741323	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12750161	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12753816	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17345170	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17345184	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17349271	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17349439	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17349467	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1936533	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2040446	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2157597	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2179491	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34248820	0.81[AMR][1000 genomes]
rs34829200	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34975352	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35091267	0.82[AMR][1000 genomes]
rs35133990	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35447001	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35458577	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3766077	0.81[EUR][1000 genomes]
rs4589164	0.81[AMR][1000 genomes]
rs4656180	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4656658	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656661	0.81[EUR][1000 genomes]
rs4656664	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4656665	0.81[EUR][1000 genomes]
rs4656669	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61806190	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61806208	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61806242	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61806244	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61808870	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61808872	0.81[EUR][1000 genomes]
rs61808874	0.84[EUR][1000 genomes]
rs745921	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7516097	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7519279	0.87[AMR][1000 genomes];0.84[EUR][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12144230	NME7	cis	Esophagus Muscularis	GTEx
rs12144230	NME7	cis	Artery Tibial	GTEx
rs12144230	NME7	cis	Thyroid	GTEx
rs12144230	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169130400-169195200	Weak transcription	Pancreas	Pancrea
2	chr1:169172400-169207600	Weak transcription	Esophagus	oesophagus
3	chr1:169172600-169227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:169173200-169202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:169176600-169206200	Weak transcription	Aorta	Aorta
6	chr1:169177400-169207400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:169180000-169210000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:169180600-169206200	Weak transcription	Left Ventricle	heart
9	chr1:169182000-169201000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:169182800-169192000	Weak transcription	Small Intestine	intestine
11	chr1:169182800-169205400	Weak transcription	Adipose Nuclei	Adipose
12	chr1:169184000-169198800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:169184400-169206200	Weak transcription	Lung	lung
14	chr1:169184600-169200600	Weak transcription	Fetal Stomach	stomach
15	chr1:169184800-169207400	Weak transcription	Ovary	ovary
16	chr1:169185000-169200800	Weak transcription	Fetal Intestine Small	intestine
17	chr1:169185800-169194400	Weak transcription	Primary B cells from cord blood	blood
18	chr1:169187600-169200200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:169187600-169207800	Weak transcription	Primary T cells from cord blood	blood
20	chr1:169187800-169194000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:169187800-169211800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:169191400-169191600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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