Variant report

Variant	rs12775041
Chromosome Location	chr10:89515818-89515819
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	chr10:89418290..89420265-chr10:89513485..89515845,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196566	Chromatin interaction
ENSG00000198682	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10082347	0.96[EUR][1000 genomes]
rs1051441	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10887748	0.89[YRI][hapmap]
rs10887749	0.89[YRI][hapmap]
rs10887750	0.88[YRI][hapmap]
rs10887753	0.94[EUR][1000 genomes]
rs11202526	0.89[YRI][hapmap]
rs11202527	0.89[YRI][hapmap]
rs11202531	0.84[EUR][1000 genomes]
rs11202536	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11202538	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11202553	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11202557	1.00[CEU][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11202563	0.94[EUR][1000 genomes]
rs11202564	0.87[CEU][hapmap]
rs11202565	0.88[EUR][1000 genomes]
rs11202568	0.91[EUR][1000 genomes]
rs11202571	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11498630	0.94[EUR][1000 genomes]
rs11812787	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11816798	0.81[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes]
rs11817759	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs11818430	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12247482	0.95[EUR][1000 genomes]
rs12253113	1.00[CEU][hapmap];0.88[CHD][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12413371	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12570131	0.94[EUR][1000 genomes]
rs12570639	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12571331	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12572346	0.84[EUR][1000 genomes]
rs12572581	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12573160	1.00[CEU][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12573349	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12762731	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs12762914	0.98[AFR][1000 genomes]
rs12764439	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12765184	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs12765681	0.95[EUR][1000 genomes]
rs12768487	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12769214	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12769771	0.89[EUR][1000 genomes]
rs12770433	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12770684	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12771188	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12771844	0.94[EUR][1000 genomes]
rs12772552	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs12773536	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12775017	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs12776656	0.98[EUR][1000 genomes]
rs12778199	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12779667	0.90[EUR][1000 genomes]
rs12779915	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs12780234	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12780237	0.81[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs12781171	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs12782128	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs12782235	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12782454	0.95[EUR][1000 genomes]
rs12783598	0.89[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs17096702	0.89[EUR][1000 genomes]
rs1819162	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1819163	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1853167	0.87[CEU][hapmap]
rs1923260	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1923261	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1923262	1.00[ASW][hapmap];0.91[CEU][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1960047	0.92[EUR][1000 genomes]
rs1993845	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2038554	0.95[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2057358	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2067661	0.90[EUR][1000 genomes]
rs2306157	0.89[EUR][1000 genomes]
rs34325090	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs34466534	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs34559481	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs34878240	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs35254974	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs35388513	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35662941	0.91[EUR][1000 genomes]
rs35814940	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3740278	0.96[EUR][1000 genomes]
rs3816651	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs4443987	0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4933461	0.89[YRI][hapmap]
rs4934363	0.89[YRI][hapmap]
rs4934364	0.89[YRI][hapmap]
rs4934366	0.89[YRI][hapmap]
rs4934367	0.89[YRI][hapmap]
rs6586102	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs66863455	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7068497	0.87[CEU][hapmap]
rs7073644	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7090088	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7090432	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7096449	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7098653	0.91[CEU][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs7480	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7481	0.86[ASW][hapmap];0.95[CEU][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7898915	0.87[CEU][hapmap]
rs7901767	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7904344	1.00[CEU][hapmap];0.88[CHD][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs7905932	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7908203	0.99[EUR][1000 genomes]
rs7910692	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7913763	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7920554	0.89[YRI][hapmap]
rs7920778	1.00[CEU][hapmap];0.88[CHD][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs7920910	0.90[EUR][1000 genomes]
rs7921017	0.87[YRI][hapmap]
rs7921889	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9651491	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9663978	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9664653	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518233	chr10:89512839-89584002	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12775041	LIPJ	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89463000-89541400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:89473000-89577200	Weak transcription	Gastric	stomach
3	chr10:89476200-89542400	Weak transcription	Pancreas	Pancrea
4	chr10:89495000-89541400	Weak transcription	Right Ventricle	heart
5	chr10:89495000-89576400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:89495200-89530600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:89495200-89542600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:89495200-89544600	Weak transcription	Brain Substantia Nigra	brain
9	chr10:89495200-89559200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr10:89495200-89577400	Weak transcription	Spleen	Spleen
11	chr10:89495400-89525600	Weak transcription	Brain Hippocampus Middle	brain
12	chr10:89498200-89519400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:89498200-89541400	Weak transcription	Aorta	Aorta
14	chr10:89498800-89536200	Weak transcription	Small Intestine	intestine
15	chr10:89503200-89521200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr10:89503400-89523200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr10:89503400-89528400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr10:89504200-89551800	Weak transcription	Psoas Muscle	Psoas
19	chr10:89505000-89520000	Weak transcription	Fetal Stomach	stomach
20	chr10:89506800-89520000	Weak transcription	Fetal Intestine Small	intestine
21	chr10:89507000-89517600	Weak transcription	Brain Angular Gyrus	brain
22	chr10:89507000-89525600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr10:89507000-89557600	Weak transcription	Lung	lung
24	chr10:89509000-89527000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr10:89510200-89553800	Weak transcription	Esophagus	oesophagus
26	chr10:89510400-89525800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr10:89510800-89519800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr10:89510800-89523000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr10:89511000-89519800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:89511000-89576800	Weak transcription	Colonic Mucosa	Colon
31	chr10:89511200-89521400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr10:89511200-89526800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr10:89511400-89518000	Strong transcription	Primary B cells from cord blood	blood
34	chr10:89511400-89521200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr10:89511600-89516400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr10:89511600-89516800	Strong transcription	Hela-S3	cervix
37	chr10:89511600-89517600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:89511600-89525600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr10:89511800-89516400	Strong transcription	A549	lung
40	chr10:89511800-89517600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr10:89512000-89516600	Strong transcription	Placenta	Placenta
42	chr10:89512000-89516600	Strong transcription	Fetal Thymus	thymus
43	chr10:89512000-89517600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr10:89512000-89520200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr10:89512000-89520400	Strong transcription	Dnd41	blood
46	chr10:89512000-89522200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr10:89512200-89516400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr10:89512400-89516400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr10:89512400-89516600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr10:89512400-89517800	Strong transcription	Primary B cells from peripheral blood	blood

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