Variant report

Variant	rs28540578
Chromosome Location	chr9:137027288-137027289
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:137003283..137007180-chr9:137027026..137030232,3	K562	blood:
2	chr9:136999027..137003702-chr9:137026566..137032835,8	MCF-7	breast:
3	chr9:136999039..137001797-chr9:137024529..137028610,4	MCF-7	breast:
4	chr9:137000597..137002215-chr9:137026002..137027594,2	K562	blood:

Variant related genes	Relation type
ENSG00000196363	Chromatin interaction
ENSG00000273249	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs28377785	1.00[EUR][1000 genomes]
rs28421319	1.00[EUR][1000 genomes]
rs28425680	1.00[EUR][1000 genomes]
rs28434714	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28436125	1.00[EUR][1000 genomes]
rs28488634	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28538491	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28562287	1.00[EUR][1000 genomes]
rs28565058	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28585632	1.00[EUR][1000 genomes]
rs28593202	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28594106	1.00[EUR][1000 genomes]
rs28595141	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28626085	1.00[EUR][1000 genomes]
rs28626885	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28637300	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28654988	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28657441	1.00[EUR][1000 genomes]
rs28673958	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28687115	1.00[EUR][1000 genomes]
rs28687158	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28701738	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705949	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28715994	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28733640	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28740804	1.00[AFR][1000 genomes]
rs28756160	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28759300	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34022301	1.00[EUR][1000 genomes]
rs34031108	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34062061	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34169579	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34259931	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34350861	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34515929	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34523253	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34856382	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35158191	1.00[EUR][1000 genomes]
rs35237188	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35370793	1.00[EUR][1000 genomes]
rs35420166	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35962164	1.00[EUR][1000 genomes]
rs35985804	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36029182	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:137007400-137027600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:137009600-137027600	Weak transcription	Fetal Brain Male	brain
3	chr9:137010600-137027600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:137013400-137028200	Weak transcription	Right Atrium	heart
5	chr9:137013600-137028200	Weak transcription	Stomach Mucosa	stomach
6	chr9:137015800-137030200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:137016400-137027800	Strong transcription	NHLF	lung
8	chr9:137016400-137029600	Weak transcription	K562	blood
9	chr9:137020400-137028600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:137021200-137027800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:137021800-137028000	Weak transcription	Psoas Muscle	Psoas
12	chr9:137021800-137028200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:137021800-137028400	Weak transcription	Fetal Kidney	kidney
14	chr9:137022000-137027800	Weak transcription	NHDF-Ad	bronchial
15	chr9:137022200-137028000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:137022400-137027800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr9:137022400-137028400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:137022400-137028400	Weak transcription	Small Intestine	intestine
19	chr9:137023400-137028000	Weak transcription	Primary B cells from cord blood	blood
20	chr9:137023400-137028400	Weak transcription	HSMMtube	muscle
21	chr9:137023800-137027800	Weak transcription	HUVEC	blood vessel
22	chr9:137023800-137028000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr9:137023800-137028400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:137023800-137028600	Weak transcription	HSMM	muscle
25	chr9:137024000-137027400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:137024000-137027800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:137024000-137027800	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:137024000-137027800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr9:137024000-137028200	Weak transcription	HMEC	breast
30	chr9:137024000-137028200	Weak transcription	Osteobl	bone
31	chr9:137024000-137028400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:137024000-137028400	Weak transcription	NH-A	brain
33	chr9:137024000-137029000	Weak transcription	A549	lung
34	chr9:137024200-137027600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:137024200-137027600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr9:137024200-137027600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:137024200-137027800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr9:137024400-137027400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:137024400-137027400	Weak transcription	Colonic Mucosa	Colon
40	chr9:137024400-137027800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr9:137024400-137027800	Weak transcription	Liver	Liver
42	chr9:137024400-137028000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr9:137024400-137028000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr9:137024400-137028000	Weak transcription	Fetal Lung	lung
45	chr9:137024400-137028000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr9:137024400-137028200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr9:137024400-137028200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:137024400-137028200	Weak transcription	Brain Angular Gyrus	brain
49	chr9:137024400-137028200	Weak transcription	Brain Anterior Caudate	brain
50	chr9:137024400-137028400	Weak transcription	Brain Substantia Nigra	brain

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