Variant report

Variant	rs28472841
Chromosome Location	chr3:113177131-113177132
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	chr3:113174583..113177246-chr3:113178980..113181235,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10511325	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11917149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11917288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11919330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11920725	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11922838	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11923128	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11924109	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11926687	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1463639	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1513288	0.87[EUR][1000 genomes]
rs16845109	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16860962	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16861014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16861023	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16861025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16861032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16861045	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16861077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16861109	0.94[EUR][1000 genomes]
rs16861217	0.80[EUR][1000 genomes]
rs17255950	0.84[EUR][1000 genomes]
rs17256551	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17256752	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17322613	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17325024	0.80[EUR][1000 genomes]
rs1906141	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1989359	0.94[EUR][1000 genomes]
rs2129431	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2129432	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271496	0.80[EUR][1000 genomes]
rs2291412	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2306068	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2306070	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35758075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35812463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56685963	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56772417	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57115529	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57164268	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57366942	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58905600	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58988763	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59271111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59493419	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59673391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60697865	0.84[EUR][1000 genomes]
rs60940543	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61065093	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61575357	0.80[EUR][1000 genomes]
rs6438150	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438151	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783691	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs735	0.84[EUR][1000 genomes]
rs7610552	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113146000-113191000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:113146200-113178600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:113147800-113178800	Weak transcription	HSMM	muscle
5	chr3:113156000-113179400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:113160200-113190000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:113160400-113186800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:113160400-113188800	Weak transcription	Colonic Mucosa	Colon
9	chr3:113160400-113191200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:113160400-113192800	Weak transcription	Stomach Mucosa	stomach
11	chr3:113160600-113178600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:113160600-113179200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:113160600-113181600	Weak transcription	Esophagus	oesophagus
14	chr3:113160600-113188600	Weak transcription	Psoas Muscle	Psoas
15	chr3:113160600-113190600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:113160600-113203800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:113160800-113179000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:113160800-113179000	Weak transcription	Brain Angular Gyrus	brain
19	chr3:113160800-113179000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:113160800-113179000	Weak transcription	HMEC	breast
21	chr3:113160800-113181200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:113160800-113187000	Weak transcription	HUVEC	blood vessel
23	chr3:113160800-113187600	Weak transcription	NHLF	lung
24	chr3:113160800-113189400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:113160800-113189400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:113160800-113189600	Weak transcription	NHEK	skin
27	chr3:113160800-113203800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:113160800-113203800	Weak transcription	Aorta	Aorta
29	chr3:113160800-113224800	Weak transcription	Placenta	Placenta
30	chr3:113160800-113232600	Weak transcription	Right Ventricle	heart
31	chr3:113161000-113179000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:113161000-113179400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:113161000-113181800	Weak transcription	Brain Anterior Caudate	brain
34	chr3:113161000-113189600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:113161000-113189600	Weak transcription	Brain Substantia Nigra	brain
36	chr3:113161000-113190800	Weak transcription	K562	blood
37	chr3:113161400-113192200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:113162200-113179000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:113164000-113185600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:113165200-113178800	Weak transcription	GM12878-XiMat	blood
41	chr3:113166200-113188800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:113166600-113186400	Weak transcription	A549	lung
43	chr3:113166600-113203800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:113166800-113178800	Weak transcription	NH-A	brain
45	chr3:113167000-113179000	Weak transcription	Fetal Kidney	kidney
46	chr3:113168200-113179000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:113169000-113186600	Weak transcription	Small Intestine	intestine
48	chr3:113169200-113179600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:113169800-113191600	Weak transcription	Fetal Brain Male	brain
50	chr3:113170600-113180000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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