Variant report

Variant	rs12145897
Chromosome Location	chr1:169116577-169116578
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	chr1:169075492..169077285-chr1:169114771..169117684,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10442644	0.95[CEU][hapmap]
rs10800407	0.83[CEU][hapmap]
rs10800411	0.83[CEU][hapmap]
rs10800418	0.82[CEU][hapmap]
rs10919075	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10919082	0.82[CEU][hapmap]
rs10919086	0.82[CEU][hapmap]
rs10919090	0.81[CEU][hapmap]
rs12067018	0.82[CEU][hapmap]
rs12067072	0.83[CEU][hapmap]
rs12072226	0.82[CEU][hapmap]
rs12072953	0.82[CEU][hapmap]
rs12075832	0.83[CEU][hapmap]
rs12076469	0.83[CEU][hapmap]
rs12080100	0.87[CEU][hapmap]
rs12081283	0.83[CEU][hapmap]
rs12082618	0.85[CEU][hapmap]
rs12083287	0.83[CEU][hapmap]
rs12084793	0.87[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12086983	0.83[CEU][hapmap]
rs12116551	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12117362	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12117559	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12118611	0.95[CEU][hapmap]
rs12120007	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12120493	0.83[CEU][hapmap]
rs12120960	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12121994	0.90[CEU][hapmap]
rs12122348	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12124168	0.81[CEU][hapmap]
rs12124738	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12125057	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12125501	0.95[CEU][hapmap]
rs12129979	0.94[CEU][hapmap]
rs12130858	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12137282	0.91[YRI][hapmap]
rs12138150	0.91[YRI][hapmap]
rs12143193	0.91[CEU][hapmap]
rs12143790	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12143963	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12143965	0.83[CEU][hapmap]
rs12144230	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12144832	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12145146	0.91[CEU][hapmap]
rs12145193	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12145226	0.91[CEU][hapmap]
rs12354315	0.82[CEU][hapmap]
rs12562404	0.82[CEU][hapmap]
rs12564596	0.83[CEU][hapmap]
rs12724802	0.83[CEU][hapmap]
rs12728614	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12730917	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12730920	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12731646	0.90[YRI][hapmap]
rs12733626	0.91[CEU][hapmap]
rs12736817	0.90[EUR][1000 genomes]
rs12740501	0.90[EUR][1000 genomes]
rs12741323	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12741540	0.82[CEU][hapmap]
rs12744184	0.82[CEU][hapmap]
rs12744341	0.82[CEU][hapmap]
rs12747242	0.83[CEU][hapmap]
rs12750161	0.90[EUR][1000 genomes]
rs12753816	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12755385	0.82[CEU][hapmap]
rs12756799	0.83[CEU][hapmap]
rs1320967	0.83[CEU][hapmap]
rs1358712	0.83[CEU][hapmap]
rs1419323	0.82[CEU][hapmap]
rs17345170	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17345184	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17349222	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs17349271	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17349439	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17349467	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1936533	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2040446	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2143287	0.83[CEU][hapmap]
rs2157597	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2179491	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2420010	0.87[CEU][hapmap]
rs34829200	0.81[EUR][1000 genomes]
rs34975352	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35133990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35220898	0.95[CEU][hapmap]
rs35447001	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35458577	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3737681	0.82[CEU][hapmap]
rs3753297	0.82[CEU][hapmap]
rs3753300	0.83[CEU][hapmap]
rs3766053	0.82[CEU][hapmap]
rs3766055	0.82[CEU][hapmap]
rs3766060	0.82[CEU][hapmap]
rs3766069	0.83[CEU][hapmap]
rs3766070	0.81[CEU][hapmap]
rs3766077	0.86[CEU][hapmap]
rs3766090	0.90[CEU][hapmap]
rs3820055	0.82[CEU][hapmap]
rs3820056	0.82[CEU][hapmap]
rs4140540	0.83[CEU][hapmap]
rs4589164	0.95[CEU][hapmap]
rs4656178	0.85[AFR][1000 genomes]
rs4656180	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4656658	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656659	0.83[CEU][hapmap]
rs4656660	0.83[CEU][hapmap]
rs4656664	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4656669	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61806190	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61806208	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61806242	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61806244	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61808870	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6427180	0.87[CEU][hapmap]
rs6703463	0.82[CEU][hapmap]
rs745921	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7516097	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7518554	0.83[CEU][hapmap]
rs7541564	0.82[CEU][hapmap]
rs7541675	0.82[CEU][hapmap]
rs7541700	0.86[CEU][hapmap]
rs909930	0.82[CEU][hapmap]
rs909931	0.82[CEU][hapmap]
rs932394	0.83[CEU][hapmap]
rs958581	0.83[CEU][hapmap]
rs9887857	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12145897	NME7	cis	Thyroid	GTEx
rs12145897	NME7	cis	Artery Tibial	GTEx
rs12145897	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs12145897	NME7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169091200-169124600	Weak transcription	NHLF	lung
2	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:169091600-169120600	Weak transcription	Lung	lung
4	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
5	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
6	chr1:169097000-169130000	Weak transcription	Ovary	ovary
7	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
9	chr1:169102000-169117400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:169102400-169120600	Weak transcription	Left Ventricle	heart
11	chr1:169103200-169117200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:169103200-169117400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:169104200-169117400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:169104800-169120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:169110400-169121800	Enhancers	Fetal Intestine Small	intestine
18	chr1:169112600-169118400	Enhancers	Stomach Mucosa	stomach
19	chr1:169112800-169120600	Weak transcription	Psoas Muscle	Psoas
20	chr1:169113600-169116800	Flanking Active TSS	A549	lung
21	chr1:169114400-169117400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:169114600-169117400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:169114800-169118200	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr1:169115000-169120600	Enhancers	HepG2	liver
25	chr1:169115000-169121200	Enhancers	Duodenum Mucosa	Duodenum
26	chr1:169115000-169121800	Enhancers	Fetal Intestine Large	intestine
27	chr1:169115200-169118000	Enhancers	Liver	Liver
28	chr1:169115400-169117800	Weak transcription	K562	blood
29	chr1:169115400-169118000	Weak transcription	Small Intestine	intestine
30	chr1:169115800-169130400	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:169116200-169117000	Enhancers	Fetal Kidney	kidney
32	chr1:169116200-169118000	Enhancers	Pancreas	Pancrea
33	chr1:169116200-169130200	Weak transcription	Brain Anterior Caudate	brain
34	chr1:169116400-169126600	Weak transcription	Right Atrium	heart
35	chr1:169116400-169139400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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