Variant report

Variant	rs4656180
Chromosome Location	chr1:169113881-169113882
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	chr1:169108245..169110163-chr1:169111975..169114283,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10081960	0.93[AFR][1000 genomes]
rs10442644	0.90[CEU][hapmap]
rs10919075	0.95[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10919082	0.81[CEU][hapmap]
rs10919090	0.81[CEU][hapmap]
rs12072953	0.82[CEU][hapmap]
rs12080100	0.81[CEU][hapmap]
rs12082618	0.85[CEU][hapmap];0.81[YRI][hapmap]
rs12084793	0.82[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12086665	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12116551	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12117362	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12117559	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12118611	0.90[CEU][hapmap]
rs12120007	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12120960	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12121994	0.85[CEU][hapmap]
rs12122348	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12124738	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12125057	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12125501	0.94[CEU][hapmap]
rs12129979	0.88[CEU][hapmap]
rs12130858	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12143193	0.86[CEU][hapmap]
rs12143790	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12143963	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12144230	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12144832	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12145146	0.86[CEU][hapmap]
rs12145193	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12145226	0.86[CEU][hapmap]
rs12145897	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12728614	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12730917	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12730920	0.85[EUR][1000 genomes]
rs12733626	0.86[CEU][hapmap]
rs12736817	0.90[EUR][1000 genomes]
rs12740501	0.90[EUR][1000 genomes]
rs12741323	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12750161	0.90[EUR][1000 genomes]
rs12752748	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12753816	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17345107	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs17345170	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17345184	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17349271	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17349439	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17349467	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1936533	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2040446	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2157597	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2179490	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs2179491	0.95[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2420008	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2420010	0.82[CEU][hapmap]
rs34829200	0.81[EUR][1000 genomes]
rs34975352	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35133990	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35220898	0.90[CEU][hapmap]
rs35447001	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35458577	0.90[EUR][1000 genomes]
rs3766070	0.80[CEU][hapmap]
rs3766077	0.81[CEU][hapmap]
rs3766090	0.85[CEU][hapmap]
rs4589164	0.90[CEU][hapmap]
rs4656177	0.83[YRI][hapmap]
rs4656658	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4656664	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs4656669	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61803315	0.93[AFR][1000 genomes]
rs61806190	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61806208	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61806242	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61806244	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61808870	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6427180	0.82[CEU][hapmap]
rs745921	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7516097	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7522760	0.89[AFR][1000 genomes]
rs7541700	0.80[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
rs4656180	NME7	cis	Artery Tibial	GTEx
rs4656180	NME7	cis	Thyroid	GTEx
rs4656180	NME7	cis	Esophagus Muscularis	GTEx
rs4656180	NME7	Cis_1M	lymphoblastoid	RTeQTL

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	chr1:169100800-169115000	Weak transcription	Small Intestine	intestine
8	chr1:169100800-169116200	Weak transcription	Fetal Kidney	kidney
9	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
11	chr1:169102000-169117400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:169102400-169120600	Weak transcription	Left Ventricle	heart
13	chr1:169102800-169114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:169103200-169116000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:169103200-169116000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:169103200-169117200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:169103200-169117400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:169103600-169114000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:169104200-169117400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:169104800-169120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:169110400-169114800	Enhancers	Fetal Intestine Large	intestine
24	chr1:169110400-169121800	Enhancers	Fetal Intestine Small	intestine
25	chr1:169110600-169114400	Enhancers	Duodenum Mucosa	Duodenum
26	chr1:169112600-169114200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr1:169112600-169118400	Enhancers	Stomach Mucosa	stomach
28	chr1:169112800-169114400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:169112800-169120600	Weak transcription	Psoas Muscle	Psoas
30	chr1:169113000-169114000	Weak transcription	Brain Angular Gyrus	brain
31	chr1:169113000-169114200	Weak transcription	K562	blood
32	chr1:169113200-169114600	Enhancers	Brain Cingulate Gyrus	brain
33	chr1:169113400-169114200	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr1:169113400-169115400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:169113600-169116800	Flanking Active TSS	A549	lung
36	chr1:169113800-169114000	Enhancers	Brain Germinal Matrix	brain
37	chr1:169113800-169114200	Flanking Active TSS	Liver	Liver
38	chr1:169113800-169114600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:169113800-169115000	Flanking Active TSS	HepG2	liver
40	chr1:169113800-169115800	Enhancers	Brain Hippocampus Middle	brain
41	chr1:169113800-169116000	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links