Variant report

Variant	rs28546404
Chromosome Location	chr4:7892822-7892823
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7880346..7881907-chr4:7891729..7893475,2	MCF-7	breast:
2	chr4:7891241..7895444-chr4:7905345..7908483,3	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10049998	0.94[ASN][1000 genomes]
rs11932843	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13115701	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13131154	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13137140	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140004	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13145572	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146302	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13147998	0.93[ASN][1000 genomes]
rs1320073	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13435273	0.94[ASN][1000 genomes]
rs17770147	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770177	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067842	0.82[ASN][1000 genomes]
rs28394221	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492032	0.82[ASN][1000 genomes]
rs28539821	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28605531	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613311	0.90[ASN][1000 genomes]
rs28631977	0.94[ASN][1000 genomes]
rs28644432	0.81[ASN][1000 genomes]
rs28673208	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28688265	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754920	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891927	0.94[ASN][1000 genomes]
rs34072304	0.94[ASN][1000 genomes]
rs34075381	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34092549	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34119140	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34121576	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34132874	0.94[ASN][1000 genomes]
rs34181918	1.00[ASN][1000 genomes]
rs34189407	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34221000	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34383852	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34392913	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34570748	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34598003	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34652148	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712341	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34868842	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869495	0.88[ASN][1000 genomes]
rs34909423	0.94[ASN][1000 genomes]
rs34982807	0.94[ASN][1000 genomes]
rs35114566	0.90[ASN][1000 genomes]
rs35138920	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35152796	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154266	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35238070	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35349192	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35502845	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35727635	1.00[ASN][1000 genomes]
rs35735994	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35881667	0.98[ASN][1000 genomes]
rs35905776	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35933973	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35967175	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36013696	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36046241	0.95[ASN][1000 genomes]
rs36106793	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934540	0.85[ASN][1000 genomes]
rs4234831	0.85[ASN][1000 genomes]
rs4256209	0.98[ASN][1000 genomes]
rs4296663	0.98[ASN][1000 genomes]
rs4361385	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4411970	0.98[ASN][1000 genomes]
rs4443285	0.85[ASN][1000 genomes]
rs4447865	0.85[ASN][1000 genomes]
rs4487321	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4579115	0.81[ASN][1000 genomes]
rs4689875	0.85[ASN][1000 genomes]
rs4696742	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4696747	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4696762	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4696772	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62289341	0.97[ASN][1000 genomes]
rs62289351	0.97[ASN][1000 genomes]
rs6446624	0.85[ASN][1000 genomes]
rs6446625	0.85[ASN][1000 genomes]
rs6446627	0.88[ASN][1000 genomes]
rs6446629	0.88[ASN][1000 genomes]
rs6824266	1.00[ASN][1000 genomes]
rs6826598	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6828574	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6829505	1.00[ASN][1000 genomes]
rs6832352	1.00[ASN][1000 genomes]
rs6833054	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6837845	1.00[ASN][1000 genomes]
rs6838055	1.00[ASN][1000 genomes]
rs6845014	1.00[ASN][1000 genomes]
rs6855982	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71600561	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71601887	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601888	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601889	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601890	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601892	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660568	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7682202	0.85[ASN][1000 genomes]
rs7682611	0.88[ASN][1000 genomes]
rs7691386	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7694106	0.94[ASN][1000 genomes]
rs7697255	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:7881800-7896600	Weak transcription	Lung	lung
6	chr4:7883200-7893000	Weak transcription	Left Ventricle	heart
7	chr4:7883200-7904400	Weak transcription	Gastric	stomach
8	chr4:7886000-7895800	Weak transcription	Esophagus	oesophagus
9	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
10	chr4:7888200-7893000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:7889200-7901200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:7890800-7893000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:7890800-7893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:7891200-7893000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:7891400-7894000	Weak transcription	Fetal Intestine Small	intestine
16	chr4:7891600-7894800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:7891600-7894800	Enhancers	Colon Smooth Muscle	Colon
18	chr4:7891600-7895000	Enhancers	NHDF-Ad	bronchial
19	chr4:7891800-7893000	Enhancers	Brain Anterior Caudate	brain
20	chr4:7891800-7893000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr4:7891800-7893200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:7891800-7893200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr4:7891800-7893400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:7891800-7893400	Enhancers	Ovary	ovary
25	chr4:7891800-7893600	Enhancers	HSMMtube	muscle
26	chr4:7891800-7893800	Enhancers	Stomach Smooth Muscle	stomach
27	chr4:7891800-7894000	Enhancers	Hela-S3	cervix
28	chr4:7891800-7894400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:7891800-7894400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr4:7891800-7894400	Enhancers	Rectal Smooth Muscle	rectum
31	chr4:7891800-7894400	Enhancers	HepG2	liver
32	chr4:7891800-7894400	Enhancers	NHEK	skin
33	chr4:7891800-7894800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr4:7891800-7894800	Enhancers	Fetal Heart	heart
35	chr4:7891800-7894800	Enhancers	HMEC	breast
36	chr4:7891800-7895000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr4:7891800-7895400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:7891800-7895800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:7892000-7893200	Enhancers	Brain Angular Gyrus	brain
40	chr4:7892000-7893600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr4:7892000-7894400	Enhancers	Brain Substantia Nigra	brain
42	chr4:7892000-7894600	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:7892000-7894600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr4:7892000-7897000	Enhancers	Brain Germinal Matrix	brain
45	chr4:7892200-7893400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:7892400-7893200	Enhancers	Brain Cingulate Gyrus	brain
47	chr4:7892400-7893400	Flanking Active TSS	A549	lung
48	chr4:7892400-7893600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:7892400-7893600	Enhancers	Adipose Nuclei	Adipose
50	chr4:7892400-7894200	Enhancers	Brain Hippocampus Middle	brain

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