Variant report

Variant	rs12117559
Chromosome Location	chr1:169214596-169214597
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169192162..169194718-chr1:169212473..169215131,2	K562	blood:
2	chr1:169208518..169210284-chr1:169213594..169216583,2	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10442644	0.81[EUR][1000 genomes]
rs10800413	0.81[EUR][1000 genomes]
rs10800418	0.81[EUR][1000 genomes]
rs10919075	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10919099	0.81[EUR][1000 genomes]
rs10919101	0.81[EUR][1000 genomes]
rs11810319	0.82[EUR][1000 genomes]
rs12080100	0.81[EUR][1000 genomes]
rs12084793	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12116551	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12116683	0.82[EUR][1000 genomes]
rs12117362	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12118611	0.82[EUR][1000 genomes]
rs12118645	0.82[EUR][1000 genomes]
rs12120007	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12120960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12122348	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12124064	0.82[EUR][1000 genomes]
rs12124738	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12125057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12125501	0.81[EUR][1000 genomes]
rs12129132	0.82[EUR][1000 genomes]
rs12129567	0.81[EUR][1000 genomes]
rs12130858	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12140995	0.81[EUR][1000 genomes]
rs12142784	0.80[EUR][1000 genomes]
rs12143790	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12143963	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12144230	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12144832	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12145193	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12145897	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12723917	0.82[EUR][1000 genomes]
rs12728614	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12730917	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12730920	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12731520	0.81[EUR][1000 genomes]
rs12736817	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12740501	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12741323	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12743588	0.82[EUR][1000 genomes]
rs12744362	0.81[EUR][1000 genomes]
rs12745978	0.82[EUR][1000 genomes]
rs12750161	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12751407	0.82[EUR][1000 genomes]
rs12751571	0.82[EUR][1000 genomes]
rs12753816	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17345170	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17345184	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17349271	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17349439	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17349467	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1936533	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2040446	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2157597	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2179491	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34248820	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34408435	0.82[EUR][1000 genomes]
rs34829200	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34975352	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35091267	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35133990	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35220898	0.82[EUR][1000 genomes]
rs35271076	0.82[EUR][1000 genomes]
rs35393101	0.82[EUR][1000 genomes]
rs35447001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35458577	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35539429	0.82[EUR][1000 genomes]
rs3766077	0.81[EUR][1000 genomes]
rs4589164	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4656180	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4656658	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4656661	0.81[EUR][1000 genomes]
rs4656664	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4656665	0.81[EUR][1000 genomes]
rs4656668	0.82[EUR][1000 genomes]
rs4656669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61806190	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61806208	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61806242	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61806244	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61808870	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61808871	0.82[EUR][1000 genomes]
rs61808872	0.83[EUR][1000 genomes]
rs61808874	0.86[EUR][1000 genomes]
rs61808916	0.82[EUR][1000 genomes]
rs61808940	0.82[EUR][1000 genomes]
rs71635617	0.82[EUR][1000 genomes]
rs72700059	0.82[EUR][1000 genomes]
rs745921	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7516097	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7519279	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 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
14	esv1792529	chr1:169207360-169241309	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv1796180	chr1:169207360-169241309	Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv1798593	chr1:169207360-169241309	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv1798636	chr1:169207360-169241309	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv1815887	chr1:169207360-169241309	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv1820986	chr1:169207360-169241309	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	esv1826976	chr1:169207360-169241309	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv1834829	chr1:169207360-169241309	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv1835188	chr1:169207360-169241309	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv1835323	chr1:169207360-169241309	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
24	esv1837297	chr1:169207360-169241309	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
25	esv1846574	chr1:169207360-169241309	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
26	esv1799599	chr1:169207360-169248783	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
27	esv1824460	chr1:169207360-169248783	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
28	esv1825991	chr1:169207360-169248783	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
29	esv1836551	chr1:169207360-169248783	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
30	esv1837116	chr1:169207360-169248783	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
31	esv1847716	chr1:169207360-169248783	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
32	esv1847725	chr1:169207360-169248783	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv1009170	chr1:169207940-169270995	Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	esv1804244	chr1:169213979-169255892	Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12117559	NME7	cis	Thyroid	GTEx
rs12117559	NME7	cis	Artery Tibial	GTEx
rs12117559	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs12117559	NME7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169172600-169227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:169210600-169215400	Weak transcription	Stomach Mucosa	stomach
3	chr1:169210800-169216600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:169214400-169214600	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr1:169214400-169214600	Flanking Active TSS	A549	lung
6	chr1:169214400-169214800	Active TSS	Ovary	ovary
7	chr1:169214400-169215200	Active TSS	Liver	Liver

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