Variant report

Variant	rs28530478
Chromosome Location	chr3:113304513-113304514
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	chr3:113304170..113307015-chr3:113318318..113321274,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072858	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12631929	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1567779	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1567781	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2048624	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271492	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271493	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271495	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2292510	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292511	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28446408	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564696	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34842926	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773691	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821682	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821683	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3896909	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3932276	0.80[EUR][1000 genomes]
rs41271363	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4560271	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4560272	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4682493	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682494	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4682496	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682497	0.81[ASN][1000 genomes]
rs55941419	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56721892	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62265514	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62265515	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62265518	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62265520	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62265521	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6787428	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72950888	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7637206	0.81[EUR][1000 genomes]
rs9816095	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9823358	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9844542	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854140	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9863703	0.80[EUR][1000 genomes]
rs9868243	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9874993	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9879239	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9985452	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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	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
2	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
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113280200-113321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:113280600-113314800	Weak transcription	Spleen	Spleen
3	chr3:113285200-113329800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:113285200-113343400	Weak transcription	Small Intestine	intestine
5	chr3:113286000-113316800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:113294400-113321600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:113296800-113324200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:113297400-113315600	Strong transcription	GM12878-XiMat	blood
9	chr3:113297800-113308000	Strong transcription	Primary T cells from cord blood	blood
10	chr3:113298800-113309400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:113298800-113315200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr3:113299400-113308000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:113299400-113315400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:113299600-113306400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:113299600-113309400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:113300800-113308800	Weak transcription	Thymus	Thymus
17	chr3:113302000-113308200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:113302200-113305400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:113302200-113308400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:113302200-113309400	Strong transcription	Primary B cells from cord blood	blood
21	chr3:113302400-113304600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:113302400-113306000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
23	chr3:113302600-113305000	Strong transcription	Fetal Thymus	thymus
24	chr3:113302800-113304800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:113302800-113305400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:113303400-113308200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr3:113303600-113305400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:113303600-113305600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:113303600-113308400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:113304000-113304800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:113304000-113304800	Enhancers	HepG2	liver
32	chr3:113304000-113305400	Enhancers	H1 Cell Line	embryonic stem cell
33	chr3:113304000-113305400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr3:113304000-113305600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr3:113304200-113305000	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:113304200-113305400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:113304200-113305400	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr3:113304200-113308000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:113304400-113304600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr3:113304400-113304800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr3:113304400-113304800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr3:113304400-113305000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:113304400-113305000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:113304400-113305000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr3:113304400-113305400	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr3:113304400-113305400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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