Variant report

Variant	rs28730729
Chromosome Location	chr1:153659860-153659861
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153651109..153660855-chr1:153698392..153702896,14	MCF-7	breast:
2	chr1:153629862..153632577-chr1:153659473..153661704,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143624	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000143553	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11264299	1.00[ASN][1000 genomes]
rs11264336	1.00[ASN][1000 genomes]
rs12076697	1.00[ASN][1000 genomes]
rs28730731	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35240348	1.00[ASN][1000 genomes]
rs3891075	1.00[ASN][1000 genomes]
rs41265168	1.00[ASN][1000 genomes]
rs55658698	1.00[ASN][1000 genomes]
rs55778008	1.00[ASN][1000 genomes]
rs56910871	1.00[ASN][1000 genomes]
rs57314764	1.00[ASN][1000 genomes]
rs57482283	1.00[ASN][1000 genomes]
rs60100741	1.00[ASN][1000 genomes]
rs60316596	1.00[ASN][1000 genomes]
rs61803563	1.00[ASN][1000 genomes]
rs61803565	1.00[ASN][1000 genomes]
rs61803566	1.00[ASN][1000 genomes]
rs61803567	1.00[ASN][1000 genomes]
rs61803571	1.00[ASN][1000 genomes]
rs61805738	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61806710	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61806714	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61806719	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427085	1.00[ASN][1000 genomes]
rs6660232	1.00[ASN][1000 genomes]
rs6663988	1.00[ASN][1000 genomes]
rs6668229	1.00[ASN][1000 genomes]
rs6672371	1.00[ASN][1000 genomes]
rs6689176	1.00[ASN][1000 genomes]
rs7512561	1.00[ASN][1000 genomes]
rs7515716	1.00[ASN][1000 genomes]
rs7520045	1.00[ASN][1000 genomes]
rs7520235	1.00[ASN][1000 genomes]
rs7533987	1.00[ASN][1000 genomes]
rs7556155	1.00[ASN][1000 genomes]
rs7556379	1.00[ASN][1000 genomes]
rs7556575	1.00[ASN][1000 genomes]
rs8532	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153652400-153664600	Weak transcription	Gastric	stomach
2	chr1:153652400-153669800	Weak transcription	Pancreas	Pancrea
3	chr1:153653000-153669800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:153653200-153664000	Weak transcription	Left Ventricle	heart
5	chr1:153653200-153669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:153653400-153663200	Strong transcription	Ovary	ovary
7	chr1:153653800-153666400	Strong transcription	Lung	lung
8	chr1:153653800-153669400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:153654400-153669200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:153654400-153669400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:153655400-153660800	Weak transcription	Spleen	Spleen
12	chr1:153655400-153669800	Weak transcription	Esophagus	oesophagus
13	chr1:153656600-153669400	Weak transcription	Fetal Kidney	kidney
14	chr1:153656800-153666400	Strong transcription	Aorta	Aorta
15	chr1:153656800-153669200	Weak transcription	A549	lung
16	chr1:153657400-153660000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:153657400-153664000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:153657800-153663400	Strong transcription	Fetal Stomach	stomach
19	chr1:153658000-153662400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:153658000-153662800	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr1:153658200-153669600	Weak transcription	Right Atrium	heart
22	chr1:153658400-153660200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:153658400-153662200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr1:153658400-153669600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:153658800-153660600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:153659000-153662200	Strong transcription	Hela-S3	cervix
27	chr1:153659400-153660000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:153659400-153662200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:153659400-153663000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:153659600-153660200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:153659600-153660600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:153659600-153661000	Genic enhancers	Adipose Nuclei	Adipose
33	chr1:153659600-153661000	Bivalent Enhancer	HepG2	liver
34	chr1:153659600-153662400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:153659600-153663000	Strong transcription	Right Ventricle	heart
36	chr1:153659800-153660400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:153659800-153669800	Weak transcription	Fetal Muscle Leg	muscle

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