Variant report

Variant	rs12084793
Chromosome Location	chr1:169115134-169115135
allele	G/T
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: 146 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10081960	0.90[AFR][1000 genomes]
rs10442644	0.81[CEU][hapmap]
rs10800407	0.96[CEU][hapmap]
rs10800411	0.95[CEU][hapmap]
rs10800418	0.95[CEU][hapmap]
rs10919075	0.87[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919082	0.95[CEU][hapmap]
rs10919086	0.95[CEU][hapmap]
rs10919090	0.95[CEU][hapmap]
rs11802143	0.92[CEU][hapmap]
rs11808938	0.92[CEU][hapmap]
rs12067018	0.95[CEU][hapmap]
rs12067072	0.96[CEU][hapmap]
rs12072226	0.95[CEU][hapmap]
rs12072953	1.00[CEU][hapmap]
rs12075832	0.96[CEU][hapmap]
rs12076469	0.96[CEU][hapmap]
rs12080100	1.00[CEU][hapmap]
rs12081283	0.96[CEU][hapmap]
rs12082618	0.95[CEU][hapmap];0.83[YRI][hapmap]
rs12083075	0.80[YRI][hapmap]
rs12083287	0.96[CEU][hapmap]
rs12086665	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12086983	0.96[CEU][hapmap];0.81[YRI][hapmap]
rs12116551	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12117362	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12117559	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12118611	0.81[CEU][hapmap]
rs12120007	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12120493	0.95[CEU][hapmap]
rs12120960	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12122348	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12123168	0.86[CEU][hapmap]
rs12124168	0.95[CEU][hapmap]
rs12124738	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12125057	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12125501	0.95[CEU][hapmap]
rs12129979	0.94[CEU][hapmap]
rs12130858	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12143790	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12143963	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12143965	0.96[CEU][hapmap]
rs12144230	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12144832	0.87[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12145193	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12145897	0.87[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12145939	0.81[YRI][hapmap]
rs12145969	0.91[CEU][hapmap]
rs12354315	0.95[CEU][hapmap]
rs12562404	0.95[CEU][hapmap]
rs12564596	0.96[CEU][hapmap]
rs12724494	0.83[YRI][hapmap]
rs12724802	0.95[CEU][hapmap]
rs12728614	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12730917	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12730920	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12736817	0.91[EUR][1000 genomes]
rs12740501	0.91[EUR][1000 genomes]
rs12741323	0.87[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12741540	0.95[CEU][hapmap]
rs12744184	0.95[CEU][hapmap]
rs12744341	0.95[CEU][hapmap]
rs12747242	0.96[CEU][hapmap]
rs12750161	0.91[EUR][1000 genomes]
rs12751062	0.91[CEU][hapmap]
rs12752748	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12753816	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12755385	0.95[CEU][hapmap]
rs12756799	0.96[CEU][hapmap]
rs12758208	0.84[CEU][hapmap]
rs1320965	0.81[YRI][hapmap]
rs1320967	0.96[CEU][hapmap]
rs1358712	0.96[CEU][hapmap]
rs1419322	0.81[YRI][hapmap]
rs1419323	0.95[CEU][hapmap]
rs17345107	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs17345170	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17345184	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17349271	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17349439	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17349467	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1936533	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2040446	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2143287	0.96[CEU][hapmap];0.81[YRI][hapmap]
rs2157597	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2179490	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2179491	0.87[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2420008	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2420010	1.00[CEU][hapmap]
rs34829200	0.82[EUR][1000 genomes]
rs34975352	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35133990	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35220898	0.82[CEU][hapmap]
rs35447001	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35458577	0.91[EUR][1000 genomes]
rs3737681	0.95[CEU][hapmap]
rs3753297	0.95[CEU][hapmap]
rs3753300	0.96[CEU][hapmap]
rs3766042	0.81[YRI][hapmap]
rs3766053	0.95[CEU][hapmap]
rs3766055	0.95[CEU][hapmap]
rs3766060	0.95[CEU][hapmap]
rs3766069	0.96[CEU][hapmap]
rs3766070	0.95[CEU][hapmap]
rs3766077	1.00[CEU][hapmap]
rs3820055	0.95[CEU][hapmap]
rs3820056	0.95[CEU][hapmap]
rs4140540	0.96[CEU][hapmap]
rs4589164	0.81[CEU][hapmap]
rs4656177	0.86[YRI][hapmap]
rs4656180	0.82[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4656181	0.91[CEU][hapmap]
rs4656656	0.95[CEU][hapmap]
rs4656658	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656659	0.96[CEU][hapmap]
rs4656660	0.96[CEU][hapmap]
rs4656664	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4656669	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61803315	0.90[AFR][1000 genomes]
rs61806190	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61806208	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61806242	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61806244	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61808870	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6427180	1.00[CEU][hapmap]
rs6688038	0.91[CEU][hapmap]
rs6688139	0.92[CEU][hapmap]
rs6703463	0.95[CEU][hapmap]
rs745921	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7516097	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7518554	0.96[CEU][hapmap]
rs7522760	0.86[AFR][1000 genomes]
rs7541564	0.95[CEU][hapmap]
rs7541675	0.95[CEU][hapmap]
rs7541700	0.86[CEU][hapmap]
rs7552484	0.81[YRI][hapmap]
rs909930	0.95[CEU][hapmap]
rs909931	0.95[CEU][hapmap]
rs932394	0.96[CEU][hapmap]
rs958581	0.96[CEU][hapmap]
rs9887857	0.96[CEU][hapmap];0.81[YRI][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
rs12084793	NME7	cis	Esophagus Muscularis	GTEx
rs12084793	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs12084793	NME7	cis	Artery Tibial	GTEx
rs12084793	NME7	cis	Thyroid	GTEx

Chromatin state (count:41 , 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	chr1:169100800-169116200	Weak transcription	Fetal Kidney	kidney
8	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
10	chr1:169102000-169117400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:169102400-169120600	Weak transcription	Left Ventricle	heart
12	chr1:169103200-169116000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:169103200-169116000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:169103200-169117200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:169103200-169117400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:169104200-169117400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:169104800-169120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:169110400-169121800	Enhancers	Fetal Intestine Small	intestine
21	chr1:169112600-169118400	Enhancers	Stomach Mucosa	stomach
22	chr1:169112800-169120600	Weak transcription	Psoas Muscle	Psoas
23	chr1:169113400-169115400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:169113600-169116800	Flanking Active TSS	A549	lung
25	chr1:169113800-169115800	Enhancers	Brain Hippocampus Middle	brain
26	chr1:169113800-169116000	Enhancers	Brain Substantia Nigra	brain
27	chr1:169114200-169115400	Enhancers	K562	blood
28	chr1:169114400-169117400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:169114600-169115200	Flanking Active TSS	Liver	Liver
30	chr1:169114600-169115200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr1:169114600-169117400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:169114800-169115200	Enhancers	Brain Angular Gyrus	brain
33	chr1:169114800-169115600	Enhancers	Brain Anterior Caudate	brain
34	chr1:169114800-169116200	Weak transcription	Pancreas	Pancrea
35	chr1:169114800-169118200	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr1:169115000-169115400	Enhancers	Brain Cingulate Gyrus	brain
37	chr1:169115000-169115400	Enhancers	Small Intestine	intestine
38	chr1:169115000-169116000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:169115000-169120600	Enhancers	HepG2	liver
40	chr1:169115000-169121200	Enhancers	Duodenum Mucosa	Duodenum
41	chr1:169115000-169121800	Enhancers	Fetal Intestine Large	intestine

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