Variant report

Variant	rs12904900
Chromosome Location	chr15:52060951-52060952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52041772..52043796-chr15:52059873..52062736,2	MCF-7	breast:
2	chr15:52058591..52061806-chr15:52062033..52065705,3	K562	blood:
3	chr15:52049744..52051270-chr15:52058518..52061301,2	K562	blood:
4	chr15:52043955..52045654-chr15:52058986..52062034,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259377	Chromatin interaction
ENSG00000128872	Chromatin interaction
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 221 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:219)

rs_ID	r²[population]
rs1025184	0.83[EUR][1000 genomes]
rs1035737	0.87[EUR][1000 genomes]
rs10444824	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10444825	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10851503	0.89[EUR][1000 genomes]
rs10851504	0.86[EUR][1000 genomes]
rs11049	0.85[EUR][1000 genomes]
rs11070865	0.87[EUR][1000 genomes]
rs11070866	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070867	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070868	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070869	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11630253	0.86[EUR][1000 genomes]
rs11630579	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630943	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631858	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11636869	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11637876	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11638677	0.85[EUR][1000 genomes]
rs12050524	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12591672	0.86[EUR][1000 genomes]
rs12593708	0.89[EUR][1000 genomes]
rs12901638	0.86[EUR][1000 genomes]
rs12903500	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12904413	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905283	0.94[EUR][1000 genomes]
rs12908327	0.89[EUR][1000 genomes]
rs12912928	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12913583	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12913850	0.89[EUR][1000 genomes]
rs12915015	0.89[EUR][1000 genomes]
rs12915568	0.89[EUR][1000 genomes]
rs17526463	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17526760	0.89[EUR][1000 genomes]
rs17539905	0.86[EUR][1000 genomes]
rs17610862	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17611193	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17612102	0.81[EUR][1000 genomes]
rs17612123	0.81[EUR][1000 genomes]
rs1840708	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1863430	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2006773	0.88[EUR][1000 genomes]
rs2007335	0.89[EUR][1000 genomes]
rs2007355	0.89[EUR][1000 genomes]
rs2010026	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2011995	0.90[EUR][1000 genomes]
rs2034856	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2052705	0.85[EUR][1000 genomes]
rs2052706	0.86[EUR][1000 genomes]
rs2052708	0.89[EUR][1000 genomes]
rs2052709	0.86[EUR][1000 genomes]
rs2114191	0.84[EUR][1000 genomes]
rs2252606	0.84[EUR][1000 genomes]
rs2252831	0.88[EUR][1000 genomes]
rs2253116	0.85[EUR][1000 genomes]
rs2303443	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2414122	0.85[EUR][1000 genomes]
rs2433217	0.86[EUR][1000 genomes]
rs2433221	0.84[EUR][1000 genomes]
rs2433222	0.86[EUR][1000 genomes]
rs2436655	0.84[EUR][1000 genomes]
rs2436656	0.85[EUR][1000 genomes]
rs2436657	0.86[EUR][1000 genomes]
rs2436658	0.84[EUR][1000 genomes]
rs2436660	0.86[EUR][1000 genomes]
rs2436662	0.88[EUR][1000 genomes]
rs2441780	0.87[EUR][1000 genomes]
rs2448946	0.86[EUR][1000 genomes]
rs2448947	0.87[EUR][1000 genomes]
rs2448948	0.86[EUR][1000 genomes]
rs2448949	0.82[EUR][1000 genomes]
rs2448950	0.86[EUR][1000 genomes]
rs2448951	0.86[EUR][1000 genomes]
rs2448953	0.85[EUR][1000 genomes]
rs2470600	0.86[EUR][1000 genomes]
rs2470601	0.87[EUR][1000 genomes]
rs2470602	0.84[EUR][1000 genomes]
rs2470608	0.86[EUR][1000 genomes]
rs2470610	0.87[EUR][1000 genomes]
rs2470611	0.86[EUR][1000 genomes]
rs2470612	0.85[EUR][1000 genomes]
rs2470616	0.83[EUR][1000 genomes]
rs2470618	0.86[EUR][1000 genomes]
rs2554314	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2554322	0.84[EUR][1000 genomes]
rs2554327	0.88[EUR][1000 genomes]
rs2554328	0.88[EUR][1000 genomes]
rs2554342	0.85[EUR][1000 genomes]
rs2554349	0.86[EUR][1000 genomes]
rs2554350	0.86[EUR][1000 genomes]
rs2554353	0.88[EUR][1000 genomes]
rs2570238	0.89[EUR][1000 genomes]
rs2570239	0.89[EUR][1000 genomes]
rs2570240	0.85[EUR][1000 genomes]
rs2570241	0.85[EUR][1000 genomes]
rs2570248	0.88[EUR][1000 genomes]
rs2570263	0.85[EUR][1000 genomes]
rs2570268	0.85[EUR][1000 genomes]
rs2570269	0.84[EUR][1000 genomes]
rs2570271	0.84[EUR][1000 genomes]
rs2570275	0.84[EUR][1000 genomes]
rs2593168	0.86[EUR][1000 genomes]
rs2593170	0.85[EUR][1000 genomes]
rs2593173	0.86[EUR][1000 genomes]
rs2593177	0.84[EUR][1000 genomes]
rs2593179	0.85[EUR][1000 genomes]
rs2593182	0.86[EUR][1000 genomes]
rs2593183	0.86[EUR][1000 genomes]
rs2593185	0.84[EUR][1000 genomes]
rs2593187	0.84[EUR][1000 genomes]
rs2593188	0.84[EUR][1000 genomes]
rs2593198	0.84[EUR][1000 genomes]
rs2593199	0.84[EUR][1000 genomes]
rs2593202	0.84[EUR][1000 genomes]
rs2623243	0.84[EUR][1000 genomes]
rs2623244	0.84[EUR][1000 genomes]
rs2623255	0.82[EUR][1000 genomes]
rs2623266	0.86[EUR][1000 genomes]
rs2623271	0.88[EUR][1000 genomes]
rs2623279	0.86[EUR][1000 genomes]
rs2623281	0.86[EUR][1000 genomes]
rs2623282	0.86[EUR][1000 genomes]
rs2623283	0.86[EUR][1000 genomes]
rs2623284	0.86[EUR][1000 genomes]
rs2623285	0.86[EUR][1000 genomes]
rs2623286	0.86[EUR][1000 genomes]
rs2623288	0.85[EUR][1000 genomes]
rs2623289	0.84[EUR][1000 genomes]
rs28699115	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2912186	0.86[EUR][1000 genomes]
rs2912187	0.85[EUR][1000 genomes]
rs2912188	0.85[EUR][1000 genomes]
rs2912189	0.86[EUR][1000 genomes]
rs2916169	0.86[EUR][1000 genomes]
rs2916170	0.85[EUR][1000 genomes]
rs2916171	0.85[EUR][1000 genomes]
rs2916172	0.87[EUR][1000 genomes]
rs2916175	0.86[EUR][1000 genomes]
rs2916176	0.86[EUR][1000 genomes]
rs2916177	0.86[EUR][1000 genomes]
rs2921951	0.86[EUR][1000 genomes]
rs2921953	0.86[EUR][1000 genomes]
rs2929422	0.85[EUR][1000 genomes]
rs2929423	0.86[EUR][1000 genomes]
rs2929424	0.85[EUR][1000 genomes]
rs2929425	0.87[EUR][1000 genomes]
rs2929426	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2929428	0.86[EUR][1000 genomes]
rs2959285	0.86[EUR][1000 genomes]
rs2959289	0.83[EUR][1000 genomes]
rs2959291	0.85[EUR][1000 genomes]
rs2959292	0.85[EUR][1000 genomes]
rs2959293	0.85[EUR][1000 genomes]
rs2959298	0.87[EUR][1000 genomes]
rs2959299	0.86[EUR][1000 genomes]
rs2959300	0.86[EUR][1000 genomes]
rs2959302	0.83[EUR][1000 genomes]
rs2959305	0.86[EUR][1000 genomes]
rs2959306	0.85[EUR][1000 genomes]
rs2959307	0.86[EUR][1000 genomes]
rs3088312	0.86[EUR][1000 genomes]
rs34098740	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34504520	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35270232	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35391204	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35823585	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36087956	0.87[EUR][1000 genomes]
rs3794532	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3898905	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4365237	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55887408	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56148956	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56185947	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62015190	0.82[EUR][1000 genomes]
rs62016192	0.86[EUR][1000 genomes]
rs6493520	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493521	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493525	0.89[EUR][1000 genomes]
rs6493526	0.88[EUR][1000 genomes]
rs67895020	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7162176	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7162554	0.84[EUR][1000 genomes]
rs7162925	0.84[EUR][1000 genomes]
rs7163541	0.84[EUR][1000 genomes]
rs7164961	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166962	0.86[EUR][1000 genomes]
rs7168659	0.86[EUR][1000 genomes]
rs7170091	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7170910	0.87[EUR][1000 genomes]
rs7171516	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7171796	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7174497	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174808	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175017	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7178166	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178561	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7178776	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7178940	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7179599	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7181540	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7182917	0.87[AMR][1000 genomes]
rs726158	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72732914	0.86[EUR][1000 genomes]
rs8024585	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8025069	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8026521	0.95[EUR][1000 genomes]
rs8027721	0.88[EUR][1000 genomes]
rs8028486	0.90[EUR][1000 genomes]
rs8028922	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8029036	0.81[EUR][1000 genomes]
rs8033433	0.88[EUR][1000 genomes]
rs8035126	0.88[EUR][1000 genomes]
rs8038344	0.90[EUR][1000 genomes]
rs8040975	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040986	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040991	0.88[EUR][1000 genomes]
rs8041866	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs990665	0.86[EUR][1000 genomes]
rs9944235	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv3411789	chr15:52052789-52087519	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52051200-52077600	Weak transcription	Psoas Muscle	Psoas
2	chr15:52051400-52061200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr15:52051400-52068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:52051400-52068400	Weak transcription	Stomach Mucosa	stomach
5	chr15:52052200-52061200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:52052200-52064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:52052200-52068200	Weak transcription	Fetal Intestine Small	intestine
8	chr15:52052200-52068600	Weak transcription	HMEC	breast
9	chr15:52052200-52074600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:52052200-52076000	Weak transcription	Fetal Brain Male	brain
11	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
12	chr15:52052400-52061000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:52052400-52067000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:52052400-52068200	Weak transcription	Fetal Intestine Large	intestine
15	chr15:52052400-52073200	Weak transcription	NHDF-Ad	bronchial
16	chr15:52052400-52078400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:52052600-52065200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:52052600-52106600	Weak transcription	HSMM	muscle
19	chr15:52053400-52090600	Weak transcription	Pancreas	Pancrea
20	chr15:52058400-52061400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:52058400-52064200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:52058400-52067600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:52058600-52068200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:52058800-52072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:52060000-52061000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr15:52060000-52061200	Enhancers	Spleen	Spleen
27	chr15:52060000-52061600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:52060000-52061600	Strong transcription	NHLF	lung
29	chr15:52060000-52061800	Strong transcription	Esophagus	oesophagus
30	chr15:52060000-52061800	Strong transcription	Dnd41	blood
31	chr15:52060000-52062600	Strong transcription	Fetal Brain Female	brain
32	chr15:52060000-52063000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:52060000-52063000	Strong transcription	Fetal Stomach	stomach
34	chr15:52060000-52063200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr15:52060000-52063600	Strong transcription	Ovary	ovary
36	chr15:52060200-52061400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:52060200-52061800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:52060200-52062400	Strong transcription	Brain Hippocampus Middle	brain
39	chr15:52060200-52062600	Strong transcription	Aorta	Aorta
40	chr15:52060200-52062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:52060200-52068200	Weak transcription	Liver	Liver
42	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:52060400-52061000	Genic enhancers	Primary T cells from cord blood	blood
44	chr15:52060400-52061200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:52060400-52061200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:52060400-52061800	Strong transcription	Pancreatic Islets	Pancreatic Islet
47	chr15:52060400-52062200	Strong transcription	Brain Cingulate Gyrus	brain
48	chr15:52060400-52062400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:52060400-52062400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:52060400-52063600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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