Variant report

Variant	rs13176320
Chromosome Location	chr5:53574002-53574003
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:53573044..53575302-chr5:53605024..53607350,2	MCF-7	breast:
2	chr5:53567065..53579931-chr5:53604839..53612520,32	K562	blood:

Variant related genes	Relation type
ENSG00000185305	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10044346	0.92[ASN][1000 genomes]
rs10077344	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10940367	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10940368	0.94[ASN][1000 genomes]
rs10940369	0.99[ASN][1000 genomes]
rs10940370	0.99[ASN][1000 genomes]
rs10940371	0.99[ASN][1000 genomes]
rs10940373	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940374	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11743476	0.97[ASN][1000 genomes]
rs11745511	0.99[ASN][1000 genomes]
rs12153418	0.98[ASN][1000 genomes]
rs12233919	0.92[ASN][1000 genomes]
rs12516888	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13180005	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13183117	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1445828	0.93[ASN][1000 genomes]
rs166093	0.89[ASN][1000 genomes]
rs17619996	0.91[ASN][1000 genomes]
rs2289853	0.93[ASN][1000 genomes]
rs2289854	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289855	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289856	0.94[ASN][1000 genomes]
rs2407405	0.92[ASN][1000 genomes]
rs250391	0.90[ASN][1000 genomes]
rs26885	0.89[ASN][1000 genomes]
rs26886	0.90[ASN][1000 genomes]
rs33282	0.88[ASN][1000 genomes]
rs35918	0.85[ASN][1000 genomes]
rs35921	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35923	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35929	0.90[AFR][1000 genomes]
rs35952	0.85[ASN][1000 genomes]
rs3776641	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3776642	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3776644	0.96[ASN][1000 genomes]
rs3776649	0.99[ASN][1000 genomes]
rs3776651	0.96[ASN][1000 genomes]
rs3797228	0.94[ASN][1000 genomes]
rs3797230	0.95[ASN][1000 genomes]
rs3797231	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797232	0.94[ASN][1000 genomes]
rs3797233	0.94[ASN][1000 genomes]
rs3797234	0.93[ASN][1000 genomes]
rs3797235	0.95[ASN][1000 genomes]
rs3797236	0.91[ASN][1000 genomes]
rs3797237	0.92[ASN][1000 genomes]
rs3797238	0.90[ASN][1000 genomes]
rs3857282	0.93[ASN][1000 genomes]
rs388337	0.88[ASN][1000 genomes]
rs3910951	0.92[ASN][1000 genomes]
rs4865810	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4865812	0.98[ASN][1000 genomes]
rs4865813	0.98[ASN][1000 genomes]
rs56854461	0.97[ASN][1000 genomes]
rs6450181	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450184	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs67553857	0.94[ASN][1000 genomes]
rs6872062	0.90[ASN][1000 genomes]
rs6872430	0.92[ASN][1000 genomes]
rs6883819	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6884123	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704911	0.94[ASN][1000 genomes]
rs7725454	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9292042	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised 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	29 gene(s)	inside rSNPs	diseases
2	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
4	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
7	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
8	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
13	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
14	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats 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	12 gene(s)	inside rSNPs	diseases
15	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
17	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
18	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv1031072	chr5:53490130-53698866	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv880304	chr5:53524508-53727092	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv598178	chr5:53566211-53600443	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53537400-53575200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:53555600-53575800	Weak transcription	Primary B cells from cord blood	blood
3	chr5:53558800-53575600	Weak transcription	Aorta	Aorta
4	chr5:53565600-53575200	Weak transcription	Fetal Stomach	stomach
5	chr5:53568200-53595600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:53569000-53575800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:53569200-53585600	Weak transcription	Fetal Thymus	thymus
8	chr5:53569600-53579400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:53569800-53583400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:53570000-53575600	Weak transcription	Lung	lung
11	chr5:53570000-53581400	Weak transcription	Right Atrium	heart
12	chr5:53570000-53591800	Weak transcription	Gastric	stomach
13	chr5:53570200-53575200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr5:53570600-53581600	Weak transcription	Fetal Lung	lung
15	chr5:53570800-53575200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:53571400-53581600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:53571800-53575800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:53571800-53577200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:53572000-53574400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:53572200-53578200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:53572400-53575400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr5:53572400-53575600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:53572400-53575600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:53572600-53575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:53572600-53575600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr5:53572600-53575600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:53573000-53576000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:53573200-53577200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:53573600-53574800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:53573600-53575600	Enhancers	K562	blood
31	chr5:53573600-53576200	Strong transcription	Primary T cells from cord blood	blood
32	chr5:53573600-53576200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:53573800-53574200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:53573800-53574200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:53573800-53574200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:53573800-53574200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr5:53573800-53574200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:53573800-53574200	Enhancers	Placenta	Placenta
39	chr5:53573800-53574200	Enhancers	Left Ventricle	heart
40	chr5:53573800-53574200	Enhancers	Pancreas	Pancrea
41	chr5:53573800-53574200	Enhancers	Right Ventricle	heart
42	chr5:53573800-53574200	Enhancers	Spleen	Spleen
43	chr5:53573800-53574600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr5:53573800-53574600	Enhancers	Fetal Intestine Small	intestine
45	chr5:53573800-53574800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:53573800-53574800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:53573800-53575000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr5:53573800-53575200	Enhancers	Fetal Intestine Large	intestine
49	chr5:53573800-53575400	Enhancers	Colon Smooth Muscle	Colon
50	chr5:53574000-53574200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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