Variant report

Variant	rs1610267
Chromosome Location	chr3:157854421-157854422
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	chr3:157833746..157835863-chr3:157852221..157854631,2	MCF-7	breast:
2	chr3:157848788..157850916-chr3:157852376..157855126,2	MCF-7	breast:

Extended variants
information (count: 121 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10470472	0.90[EUR][1000 genomes]
rs1095636	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11715599	0.82[ASN][1000 genomes]
rs1193511	0.90[EUR][1000 genomes]
rs1193513	0.90[EUR][1000 genomes]
rs1193536	0.89[EUR][1000 genomes]
rs1204957	0.91[EUR][1000 genomes]
rs12485440	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12486461	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12634832	0.83[EUR][1000 genomes]
rs12696067	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13059066	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13061378	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1581408	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1608100	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1608101	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1609525	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1609526	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1610266	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610268	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724666	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1724679	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1729998	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1730008	0.88[EUR][1000 genomes]
rs1730029	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1730032	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1730039	0.90[EUR][1000 genomes]
rs1730041	0.88[EUR][1000 genomes]
rs1730044	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1730099	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1915935	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2682402	0.91[EUR][1000 genomes]
rs2682407	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2693540	0.91[EUR][1000 genomes]
rs2693546	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4261830	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4317053	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4346508	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4414801	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4431056	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4602343	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4622858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4642075	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680411	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680412	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680413	0.97[ASN][1000 genomes]
rs57665991	0.97[ASN][1000 genomes]
rs6441174	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6762706	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770442	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6773505	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6783175	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6789448	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6790608	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6794461	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6797626	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6800218	0.81[ASN][1000 genomes]
rs6803532	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6803630	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs696715	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs698975	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs698976	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs698977	0.92[EUR][1000 genomes]
rs698979	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs698981	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs698982	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs698983	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs698984	0.90[EUR][1000 genomes]
rs698985	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs698992	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs699918	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs699923	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs699925	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs699926	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7614572	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618071	0.86[EUR][1000 genomes]
rs7622971	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624303	0.97[ASN][1000 genomes]
rs7630176	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7647342	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653039	0.92[EUR][1000 genomes]
rs827104	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs827130	0.91[EUR][1000 genomes]
rs827139	0.91[EUR][1000 genomes]
rs827141	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827142	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827145	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs827146	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827147	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827149	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827153	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827155	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827157	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827160	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827162	0.90[EUR][1000 genomes]
rs827168	0.90[EUR][1000 genomes]
rs827170	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs827173	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827174	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827801	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827805	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs844141	0.88[EUR][1000 genomes]
rs860422	0.91[EUR][1000 genomes]
rs862352	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs864331	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs864876	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs866657	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9290020	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9290021	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814942	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9820954	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9848433	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9862337	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9870745	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871021	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9881063	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9883891	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers 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
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1610267	RP11-538P18.2	cis	lung	GTEx
rs1610267	RP11-538P18.2	cis	Artery Tibial	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157828600-157857000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:157829200-157861400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:157830000-157866400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:157833200-157856200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:157836600-157854600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:157837600-157877600	Weak transcription	Fetal Heart	heart
7	chr3:157838800-157862600	Weak transcription	Pancreas	Pancrea
8	chr3:157840200-157856000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:157840800-157856200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:157842800-157855600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:157842800-157855600	Weak transcription	Fetal Stomach	stomach
12	chr3:157842800-157855800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:157842800-157856400	Weak transcription	Placenta	Placenta
14	chr3:157842800-157856800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:157842800-157858000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:157842800-157858200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:157843000-157868600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:157843400-157856600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:157843600-157857200	Weak transcription	HepG2	liver
20	chr3:157843600-157866200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:157843600-157886800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:157845800-157857600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:157846000-157857400	Weak transcription	Spleen	Spleen
24	chr3:157846000-157860800	Weak transcription	Small Intestine	intestine
25	chr3:157846000-157868400	Weak transcription	Lung	lung
26	chr3:157846000-157869200	Weak transcription	Esophagus	oesophagus
27	chr3:157846200-157855800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:157846200-157857200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:157846200-157857200	Weak transcription	Brain Substantia Nigra	brain
30	chr3:157846200-157857400	Weak transcription	NHDF-Ad	bronchial
31	chr3:157846200-157857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:157846200-157857800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:157846200-157859200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:157846200-157861800	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:157846200-157862800	Weak transcription	Fetal Brain Female	brain
36	chr3:157846200-157869200	Weak transcription	Psoas Muscle	Psoas
37	chr3:157846200-157869200	Weak transcription	NHEK	skin
38	chr3:157846200-157872000	Weak transcription	Primary T cells from cord blood	blood
39	chr3:157846200-157875200	Weak transcription	Gastric	stomach
40	chr3:157846200-157893400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:157846200-157893600	Weak transcription	Aorta	Aorta
42	chr3:157846600-157855800	Weak transcription	Hela-S3	cervix
43	chr3:157846600-157858000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:157846600-157867400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:157846600-157878600	Weak transcription	HSMM	muscle
46	chr3:157846800-157854600	Weak transcription	Brain Anterior Caudate	brain
47	chr3:157846800-157857200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:157846800-157857600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:157846800-157860200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:157846800-157860200	Weak transcription	Left Ventricle	heart

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