Variant report

Variant	rs28562287
Chromosome Location	chr9:137007451-137007452
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	chr9:136931362..136933512-chr9:137005797..137009467,3	MCF-7	breast:
2	chr9:137006870..137008925-chr9:137009202..137011699,2	K562	blood:

Variant related genes	Relation type
ENSG00000169925	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs28377785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28399690	1.00[AFR][1000 genomes]
rs28421319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28425680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434714	1.00[EUR][1000 genomes]
rs28436125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28452481	1.00[AFR][1000 genomes]
rs28488634	1.00[EUR][1000 genomes]
rs28538491	1.00[EUR][1000 genomes]
rs28540578	1.00[EUR][1000 genomes]
rs28562957	1.00[AFR][1000 genomes]
rs28565058	1.00[EUR][1000 genomes]
rs28585632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28593202	1.00[EUR][1000 genomes]
rs28594106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595141	1.00[EUR][1000 genomes]
rs28626085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28626885	1.00[EUR][1000 genomes]
rs28637300	1.00[EUR][1000 genomes]
rs28654988	1.00[EUR][1000 genomes]
rs28657441	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28673958	1.00[EUR][1000 genomes]
rs28687115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28687158	0.96[EUR][1000 genomes]
rs28701738	1.00[EUR][1000 genomes]
rs28705949	1.00[EUR][1000 genomes]
rs28708401	1.00[AFR][1000 genomes]
rs28715994	1.00[EUR][1000 genomes]
rs28733640	1.00[EUR][1000 genomes]
rs28756160	1.00[EUR][1000 genomes]
rs28759300	1.00[EUR][1000 genomes]
rs34022301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34031108	1.00[EUR][1000 genomes]
rs34062061	1.00[EUR][1000 genomes]
rs34169579	1.00[EUR][1000 genomes]
rs34194763	1.00[AFR][1000 genomes]
rs34259931	0.89[EUR][1000 genomes]
rs34350861	1.00[EUR][1000 genomes]
rs34515929	1.00[EUR][1000 genomes]
rs34523253	1.00[EUR][1000 genomes]
rs34546899	1.00[AFR][1000 genomes]
rs34856382	1.00[EUR][1000 genomes]
rs34929179	1.00[AFR][1000 genomes]
rs35158191	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35237188	1.00[EUR][1000 genomes]
rs35370793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35420166	1.00[EUR][1000 genomes]
rs35504753	1.00[AFR][1000 genomes]
rs35511305	1.00[AFR][1000 genomes]
rs35874066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35924689	1.00[AFR][1000 genomes]
rs35962164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35985804	0.92[EUR][1000 genomes]
rs36029182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71483222	1.00[AFR][1000 genomes]
rs71505283	1.00[AFR][1000 genomes]
rs71505284	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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 target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active 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	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
7	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:137002400-137016200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:137003200-137024200	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:137003600-137007600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:137003600-137024800	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr9:137004000-137017400	Strong transcription	HUVEC	blood vessel
6	chr9:137004000-137024000	Strong transcription	A549	lung
7	chr9:137004000-137024800	Strong transcription	Primary T cells from cord blood	blood
8	chr9:137004200-137015800	Weak transcription	Fetal Heart	heart
9	chr9:137004200-137016000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:137004200-137024400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:137004200-137024800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:137004200-137024800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr9:137004200-137025000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:137004200-137025000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr9:137004200-137026000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr9:137004400-137010800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:137004400-137011800	Weak transcription	Small Intestine	intestine
18	chr9:137004400-137013600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:137004400-137014200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:137004400-137024800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:137004400-137025800	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr9:137004400-137025800	Strong transcription	Fetal Thymus	thymus
23	chr9:137004600-137009200	Weak transcription	Psoas Muscle	Psoas
24	chr9:137004600-137010400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:137004600-137010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr9:137004600-137010800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:137004600-137011600	Strong transcription	HMEC	breast
28	chr9:137004600-137011600	Strong transcription	NHEK	skin
29	chr9:137004600-137015000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr9:137004600-137016200	Strong transcription	Spleen	Spleen
31	chr9:137004600-137024400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:137004600-137024600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr9:137004600-137024800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:137004600-137024800	Strong transcription	Gastric	stomach
35	chr9:137004600-137025000	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr9:137004600-137025000	Strong transcription	Dnd41	blood
37	chr9:137004600-137025800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:137004600-137026000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:137004600-137026200	Strong transcription	Fetal Intestine Large	intestine
40	chr9:137004600-137026200	Strong transcription	Hela-S3	cervix
41	chr9:137004600-137026400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:137004800-137009400	Strong transcription	HSMM	muscle
43	chr9:137004800-137024200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:137004800-137025000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr9:137004800-137025000	Strong transcription	Fetal Brain Female	brain
46	chr9:137004800-137025600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:137004800-137026400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:137004800-137026400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr9:137005000-137008000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr9:137005000-137009800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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