Variant report

Variant	rs12253113
Chromosome Location	chr10:89512839-89512840
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	chr10:89511205..89513054-chr10:89516140..89517793,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10082347	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10218936	0.81[AMR][1000 genomes]
rs1051441	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10887753	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11202531	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11202536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11202538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202553	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11202557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11202563	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11202564	0.87[CEU][hapmap]
rs11202565	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11202568	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11202571	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11498630	0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11812787	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11816798	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11817759	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11818430	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12247482	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12413371	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12570131	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12570639	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12571331	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12572346	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12572581	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12573160	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12573349	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12762731	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12764439	0.83[EUR][1000 genomes]
rs12765184	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12765681	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12768487	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12769214	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12769771	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12770433	0.86[EUR][1000 genomes]
rs12770684	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12771188	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12771844	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12772552	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12773536	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12775017	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12775041	1.00[CEU][hapmap];0.88[CHD][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12776656	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12778199	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12779667	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12779915	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12780234	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12780237	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12781171	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12782128	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12782235	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12782454	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12783598	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1321934	0.89[MEX][hapmap]
rs17096702	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1819162	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1819163	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1853167	0.87[CEU][hapmap]
rs1923260	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1923261	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1923262	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1960047	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1993845	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2038554	0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2057358	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2067661	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2306157	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34325090	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34466534	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34559481	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34878240	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35254974	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35388513	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35662941	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35814940	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740278	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781187	0.86[YRI][hapmap]
rs3816651	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4443987	0.90[EUR][1000 genomes]
rs6586102	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66863455	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7068497	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs7073644	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7090088	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7090432	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7096449	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098653	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7480	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7481	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898915	0.87[CEU][hapmap]
rs7901767	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7904344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7905932	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7908203	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910692	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7913763	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7920778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7920910	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7921889	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9651491	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9663978	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9664653	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[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
rs12253113	LIPJ	cis	cerebellum	SCAN

Chromatin state (count:119 , 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	chr10:89495000-89514000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr10:89495000-89541400	Weak transcription	Right Ventricle	heart
6	chr10:89495000-89576400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:89495200-89514000	Weak transcription	Fetal Muscle Leg	muscle
8	chr10:89495200-89515600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr10:89495200-89530600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:89495200-89542600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:89495200-89544600	Weak transcription	Brain Substantia Nigra	brain
12	chr10:89495200-89559200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr10:89495200-89577400	Weak transcription	Spleen	Spleen
14	chr10:89495400-89525600	Weak transcription	Brain Hippocampus Middle	brain
15	chr10:89495600-89513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr10:89498200-89519400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr10:89498200-89541400	Weak transcription	Aorta	Aorta
18	chr10:89498800-89536200	Weak transcription	Small Intestine	intestine
19	chr10:89500600-89513000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr10:89503200-89521200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:89503400-89523200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:89503400-89528400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr10:89503600-89513600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr10:89503600-89515600	Weak transcription	HepG2	liver
25	chr10:89504200-89551800	Weak transcription	Psoas Muscle	Psoas
26	chr10:89505000-89520000	Weak transcription	Fetal Stomach	stomach
27	chr10:89505600-89514000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr10:89506800-89513600	Weak transcription	Adipose Nuclei	Adipose
29	chr10:89506800-89513800	Weak transcription	Ovary	ovary
30	chr10:89506800-89514000	Weak transcription	Left Ventricle	heart
31	chr10:89506800-89520000	Weak transcription	Fetal Intestine Small	intestine
32	chr10:89507000-89513600	Weak transcription	Brain Anterior Caudate	brain
33	chr10:89507000-89513600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr10:89507000-89515400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr10:89507000-89517600	Weak transcription	Brain Angular Gyrus	brain
36	chr10:89507000-89525600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr10:89507000-89557600	Weak transcription	Lung	lung
38	chr10:89507200-89513800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:89507400-89514000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr10:89508600-89513800	Weak transcription	Fetal Lung	lung
41	chr10:89509000-89527000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr10:89509200-89514000	Weak transcription	Primary T cells from cord blood	blood
43	chr10:89510000-89513000	Weak transcription	NH-A	brain
44	chr10:89510000-89513200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:89510000-89514000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr10:89510000-89514000	Weak transcription	HSMMtube	muscle
47	chr10:89510000-89515400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr10:89510000-89515800	Weak transcription	K562	blood
49	chr10:89510200-89513000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr10:89510200-89513600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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