Variant report

Variant	rs28694456
Chromosome Location	chr4:152045368-152045369
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	chr4:152020934..152022661-chr4:152043447..152045855,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145425	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10009307	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940627	0.84[ASN][1000 genomes]
rs12501643	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280283	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28593016	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36115072	0.81[ASN][1000 genomes]
rs3736502	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762846	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535764	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847518	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6858302	0.83[ASN][1000 genomes]
rs72963696	0.84[ASN][1000 genomes]
rs7656771	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7675432	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7681571	0.81[ASN][1000 genomes]
rs7682480	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7699495	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1018404	chr4:151664438-152067409	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1017850	chr4:151664438-152071876	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv2763837	chr4:151664438-152071888	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv870257	chr4:151665349-152072867	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1015387	chr4:151673751-152071876	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv526976	chr4:151675819-152055073	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv949066	chr4:151693149-152069566	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv949002	chr4:151693149-152095109	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1031720	chr4:151708502-152071876	Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
15	nsv1031516	chr4:151718614-152065644	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
16	nsv537304	chr4:151718614-152065644	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
17	nsv1022884	chr4:151718814-152065505	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
18	nsv537305	chr4:151718814-152065505	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
19	nsv595690	chr4:151788955-152109552	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
20	nsv1026416	chr4:151847403-152105879	Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
21	nsv1018797	chr4:151913585-152073419	Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
22	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
23	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
24	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152022800-152069800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:152025000-152073200	Weak transcription	Stomach Mucosa	stomach
3	chr4:152025200-152073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:152025200-152085400	Weak transcription	Hela-S3	cervix
5	chr4:152027000-152086600	Weak transcription	Fetal Kidney	kidney
6	chr4:152027200-152050400	Weak transcription	Aorta	Aorta
7	chr4:152027200-152095600	Weak transcription	Pancreas	Pancrea
8	chr4:152027800-152047200	Weak transcription	HSMMtube	muscle
9	chr4:152027800-152050800	Weak transcription	Spleen	Spleen
10	chr4:152027800-152065000	Weak transcription	Gastric	stomach
11	chr4:152028000-152047200	Weak transcription	Esophagus	oesophagus
12	chr4:152028600-152048600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:152028600-152065600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:152028800-152049000	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:152029200-152046000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:152029200-152047200	Weak transcription	Brain Angular Gyrus	brain
17	chr4:152029200-152048400	Weak transcription	HMEC	breast
18	chr4:152029200-152060800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:152029200-152065200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:152029200-152070600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:152031800-152048600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:152031800-152052800	Weak transcription	Fetal Brain Female	brain
23	chr4:152033000-152059000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:152033400-152045600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:152034200-152048400	Weak transcription	A549	lung
26	chr4:152034400-152046000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:152034800-152050600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:152035000-152048400	Weak transcription	Brain Substantia Nigra	brain
29	chr4:152035200-152047000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:152035600-152072400	Weak transcription	Fetal Brain Male	brain
31	chr4:152036000-152046400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:152036000-152047200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:152036200-152047200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:152036600-152058400	Weak transcription	Fetal Heart	heart
35	chr4:152036800-152049200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:152039000-152046600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:152039000-152047200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:152039400-152058600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:152039800-152051200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:152040200-152046800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:152040200-152065800	Strong transcription	Adipose Nuclei	Adipose
42	chr4:152040400-152051600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr4:152040400-152067200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:152040400-152073800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:152040800-152046400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:152040800-152056400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr4:152041400-152047200	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:152041400-152047200	Weak transcription	Right Ventricle	heart
49	chr4:152041600-152052000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr4:152042000-152047200	Weak transcription	HSMM	muscle

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