Variant report

Variant	rs28479377
Chromosome Location	chr9:137027712-137027713
allele	C/T
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:

Variant related genes	Relation type
ENSG00000273249	Chromatin interaction
ENSG00000196363	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs28360858	1.00[EUR][1000 genomes]
rs28399690	1.00[EUR][1000 genomes]
rs28401385	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28412245	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28440102	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28442241	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28452481	1.00[EUR][1000 genomes]
rs28473171	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28491791	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28507057	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28510444	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28523906	0.90[AFR][1000 genomes]
rs28562957	1.00[EUR][1000 genomes]
rs28572025	0.91[AFR][1000 genomes]
rs28579703	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28620240	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28626222	0.90[AFR][1000 genomes]
rs28637761	0.92[AFR][1000 genomes]
rs28705689	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705949	0.93[AFR][1000 genomes]
rs28708401	1.00[EUR][1000 genomes]
rs28710163	1.00[EUR][1000 genomes]
rs28712382	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28714237	1.00[EUR][1000 genomes]
rs28740804	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28758854	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28759300	0.90[AFR][1000 genomes]
rs28759311	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34062061	0.89[AFR][1000 genomes]
rs34079254	1.00[EUR][1000 genomes]
rs34194763	1.00[EUR][1000 genomes]
rs34473303	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34546899	1.00[EUR][1000 genomes]
rs34607253	0.92[EUR][1000 genomes]
rs34646496	1.00[EUR][1000 genomes]
rs34861636	1.00[EUR][1000 genomes]
rs34929179	1.00[EUR][1000 genomes]
rs35209649	1.00[EUR][1000 genomes]
rs35322411	1.00[EUR][1000 genomes]
rs35387289	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35419030	1.00[EUR][1000 genomes]
rs35448798	1.00[EUR][1000 genomes]
rs35487246	0.84[EUR][1000 genomes]
rs35489314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35504753	1.00[EUR][1000 genomes]
rs35511305	1.00[EUR][1000 genomes]
rs35709000	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35726748	1.00[EUR][1000 genomes]
rs35924689	1.00[EUR][1000 genomes]
rs58124205	0.87[AFR][1000 genomes]
rs71483222	1.00[EUR][1000 genomes]
rs71505283	1.00[EUR][1000 genomes]
rs71505284	1.00[EUR][1000 genomes]
rs73663200	0.87[AFR][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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:137013400-137028200	Weak transcription	Right Atrium	heart
2	chr9:137013600-137028200	Weak transcription	Stomach Mucosa	stomach
3	chr9:137015800-137030200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:137016400-137027800	Strong transcription	NHLF	lung
5	chr9:137016400-137029600	Weak transcription	K562	blood
6	chr9:137020400-137028600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:137021200-137027800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:137021800-137028000	Weak transcription	Psoas Muscle	Psoas
9	chr9:137021800-137028200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:137021800-137028400	Weak transcription	Fetal Kidney	kidney
11	chr9:137022000-137027800	Weak transcription	NHDF-Ad	bronchial
12	chr9:137022200-137028000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr9:137022400-137027800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr9:137022400-137028400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:137022400-137028400	Weak transcription	Small Intestine	intestine
16	chr9:137023400-137028000	Weak transcription	Primary B cells from cord blood	blood
17	chr9:137023400-137028400	Weak transcription	HSMMtube	muscle
18	chr9:137023800-137027800	Weak transcription	HUVEC	blood vessel
19	chr9:137023800-137028000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr9:137023800-137028400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:137023800-137028600	Weak transcription	HSMM	muscle
22	chr9:137024000-137027800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr9:137024000-137027800	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:137024000-137027800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:137024000-137028200	Weak transcription	HMEC	breast
26	chr9:137024000-137028200	Weak transcription	Osteobl	bone
27	chr9:137024000-137028400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:137024000-137028400	Weak transcription	NH-A	brain
29	chr9:137024000-137029000	Weak transcription	A549	lung
30	chr9:137024200-137027800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:137024400-137027800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:137024400-137027800	Weak transcription	Liver	Liver
33	chr9:137024400-137028000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr9:137024400-137028000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr9:137024400-137028000	Weak transcription	Fetal Lung	lung
36	chr9:137024400-137028000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:137024400-137028200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr9:137024400-137028200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr9:137024400-137028200	Weak transcription	Brain Angular Gyrus	brain
40	chr9:137024400-137028200	Weak transcription	Brain Anterior Caudate	brain
41	chr9:137024400-137028400	Weak transcription	Brain Substantia Nigra	brain
42	chr9:137024600-137027800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr9:137024600-137028000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr9:137024600-137028000	Weak transcription	Adipose Nuclei	Adipose
45	chr9:137024600-137028000	Weak transcription	Ovary	ovary
46	chr9:137024600-137028200	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:137024600-137028200	Weak transcription	Thymus	Thymus
48	chr9:137024800-137027800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:137024800-137027800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr9:137024800-137028000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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