Variant report

Variant	rs12095171
Chromosome Location	chr1:169114829-169114830
allele	C/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: 166 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs10081959	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10800403	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800406	1.00[ASN][1000 genomes]
rs10800407	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10800410	0.84[ASN][1000 genomes]
rs10800411	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs1080267	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10919065	0.82[CHB][hapmap]
rs10919073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919076	1.00[ASN][1000 genomes]
rs10919082	0.82[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs10919083	0.93[ASN][1000 genomes]
rs10919084	0.93[ASN][1000 genomes]
rs10919086	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs10919090	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs10919094	0.84[ASN][1000 genomes]
rs1138486	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11801853	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11802117	0.93[ASN][1000 genomes]
rs11809180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12057856	0.93[ASN][1000 genomes]
rs12065884	0.93[ASN][1000 genomes]
rs12066676	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12067018	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs12067072	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs12070626	0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12071277	0.86[ASN][1000 genomes]
rs12072226	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs12072953	0.93[ASN][1000 genomes]
rs12075832	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs12076469	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs12076510	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12079745	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12082618	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12082810	1.00[ASN][1000 genomes]
rs12083075	0.82[CHB][hapmap]
rs12083287	0.91[CHB][hapmap]
rs12084964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086292	0.86[ASN][1000 genomes]
rs12086983	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12089118	1.00[ASN][1000 genomes]
rs12120493	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs12124144	0.93[ASN][1000 genomes]
rs12124168	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs12124744	0.85[ASN][1000 genomes]
rs12125921	0.93[ASN][1000 genomes]
rs12125985	0.93[ASN][1000 genomes]
rs12126032	0.86[ASN][1000 genomes]
rs12127305	0.86[ASN][1000 genomes]
rs12127613	0.91[ASN][1000 genomes]
rs12129969	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs12129979	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12130764	0.84[ASN][1000 genomes]
rs12135928	1.00[ASN][1000 genomes]
rs12140967	1.00[ASN][1000 genomes]
rs12143131	1.00[ASN][1000 genomes]
rs12143135	0.88[ASN][1000 genomes]
rs12143965	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs12144705	0.89[ASN][1000 genomes]
rs12145939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12354315	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12562404	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs12564558	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12564596	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs12568636	0.84[ASN][1000 genomes]
rs12691502	0.82[CHB][hapmap]
rs12724494	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12724802	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs12724812	0.93[ASN][1000 genomes]
rs12724863	0.84[ASN][1000 genomes]
rs12728466	0.82[CHB][hapmap]
rs12734206	0.84[ASN][1000 genomes]
rs12735503	0.93[ASN][1000 genomes]
rs12736110	0.93[ASN][1000 genomes]
rs12736723	0.84[ASN][1000 genomes]
rs12744184	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs12744341	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs12744655	0.97[ASN][1000 genomes]
rs12745732	0.87[ASN][1000 genomes]
rs12747242	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs12751379	1.00[CEU][hapmap]
rs12753710	1.00[CEU][hapmap]
rs12755385	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs12756799	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs12758208	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1320965	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1320966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320967	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1320968	1.00[ASN][1000 genomes]
rs1358712	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1419322	0.82[CHB][hapmap]
rs1419323	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1419324	1.00[ASN][1000 genomes]
rs16862051	1.00[CEU][hapmap]
rs1830492	0.83[ASN][1000 genomes]
rs1830494	0.83[ASN][1000 genomes]
rs1830495	0.92[ASN][1000 genomes]
rs2032044	0.86[ASN][1000 genomes]
rs2050119	0.93[ASN][1000 genomes]
rs2143287	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2179492	0.84[ASN][1000 genomes]
rs2420010	0.97[ASN][1000 genomes]
rs2901029	0.82[CHB][hapmap]
rs34250651	0.93[ASN][1000 genomes]
rs34605921	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34645703	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34847919	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35037551	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35631014	0.93[ASN][1000 genomes]
rs35774511	0.93[ASN][1000 genomes]
rs3737681	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs3766045	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766053	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3766054	1.00[ASN][1000 genomes]
rs3766055	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3766059	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs3766060	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs3766061	0.80[ASN][1000 genomes]
rs3766062	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs3766063	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766065	0.84[ASN][1000 genomes]
rs3766066	0.84[ASN][1000 genomes]
rs3766067	0.84[ASN][1000 genomes]
rs3766069	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs3766070	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs3766071	0.84[ASN][1000 genomes]
rs3820053	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs3820055	0.91[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs3820056	0.91[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs4140540	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs4656653	1.00[ASN][1000 genomes]
rs4656654	0.93[ASN][1000 genomes]
rs4656655	0.93[ASN][1000 genomes]
rs4656656	0.80[CHB][hapmap];0.93[ASN][1000 genomes]
rs4656659	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs4656660	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs61806209	0.90[ASN][1000 genomes]
rs6695177	0.93[ASN][1000 genomes]
rs6695252	0.93[ASN][1000 genomes]
rs67485965	0.93[ASN][1000 genomes]
rs72637225	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs745922	1.00[ASN][1000 genomes]
rs7518554	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs7528751	1.00[CEU][hapmap]
rs7529937	0.97[ASN][1000 genomes]
rs7541564	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs7541675	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs7541700	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs7552484	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs909929	0.91[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs909930	0.91[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs909931	0.91[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs932394	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs932395	0.93[ASN][1000 genomes]
rs958581	0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs968304	0.82[CHB][hapmap]
rs9887854	1.00[ASN][1000 genomes]
rs9887857	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9887903	1.00[ASN][1000 genomes]
rs9887916	0.98[ASN][1000 genomes]

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

No data

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

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