Variant report

Variant	rs28705689
Chromosome Location	chr9:137019409-137019410
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:137017573..137021072-chr9:137021184..137024307,5	K562	blood:
2	chr9:136999617..137003086-chr9:137017265..137019661,4	MCF-7	breast:
3	chr9:137011015..137015920-chr9:137017197..137019445,5	K562	blood:
4	chr9:137016596..137020478-chr9:137022526..137026259,4	K562	blood:
5	chr9:136999814..137001469-chr9:137019178..137021938,2	K562	blood:
6	chr9:137002821..137008342-chr9:137016004..137020926,8	MCF-7	breast:
7	chr9:137012358..137014915-chr9:137017320..137020434,5	K562	blood:

Variant related genes	Relation type
ENSG00000196363	Chromatin interaction
ENSG00000273249	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs28360858	1.00[EUR][1000 genomes]
rs28399690	1.00[EUR][1000 genomes]
rs28401385	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28412245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28440102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28442241	0.83[AFR][1000 genomes]
rs28452481	1.00[EUR][1000 genomes]
rs28473171	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28479377	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28491791	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28507057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28510444	0.94[AFR][1000 genomes]
rs28523906	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28562957	1.00[EUR][1000 genomes]
rs28572025	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28579703	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28620240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28626222	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28637077	0.87[AMR][1000 genomes]
rs28637761	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28657551	0.87[AMR][1000 genomes]
rs28705949	1.00[AFR][1000 genomes]
rs28708401	1.00[EUR][1000 genomes]
rs28710163	1.00[EUR][1000 genomes]
rs28712382	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28714237	1.00[EUR][1000 genomes]
rs28726357	0.87[AMR][1000 genomes]
rs28740804	1.00[EUR][1000 genomes]
rs28758854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28759300	0.97[AFR][1000 genomes]
rs28759311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34062061	0.96[AFR][1000 genomes]
rs34079254	1.00[EUR][1000 genomes]
rs34194763	1.00[EUR][1000 genomes]
rs34473303	1.00[AFR][1000 genomes];1.00[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	1.00[AFR][1000 genomes];1.00[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	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35504753	1.00[EUR][1000 genomes]
rs35511305	1.00[EUR][1000 genomes]
rs35709000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35726748	1.00[EUR][1000 genomes]
rs35924689	1.00[EUR][1000 genomes]
rs58124205	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58734062	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs71483222	1.00[EUR][1000 genomes]
rs71505283	1.00[EUR][1000 genomes]
rs71505284	1.00[EUR][1000 genomes]
rs73663200	0.94[AFR][1000 genomes];0.87[AMR][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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:137003200-137024200	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:137003600-137024800	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr9:137004000-137024000	Strong transcription	A549	lung
4	chr9:137004000-137024800	Strong transcription	Primary T cells from cord blood	blood
5	chr9:137004200-137024400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr9:137004200-137024800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:137004200-137024800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr9:137004200-137025000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:137004200-137025000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr9:137004200-137026000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:137004400-137024800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:137004400-137025800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr9:137004400-137025800	Strong transcription	Fetal Thymus	thymus
14	chr9:137004600-137024400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr9:137004600-137024600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:137004600-137024800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:137004600-137024800	Strong transcription	Gastric	stomach
18	chr9:137004600-137025000	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr9:137004600-137025000	Strong transcription	Dnd41	blood
20	chr9:137004600-137025800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:137004600-137026000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:137004600-137026200	Strong transcription	Fetal Intestine Large	intestine
23	chr9:137004600-137026200	Strong transcription	Hela-S3	cervix
24	chr9:137004600-137026400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:137004800-137024200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:137004800-137025000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr9:137004800-137025000	Strong transcription	Fetal Brain Female	brain
28	chr9:137004800-137025600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:137004800-137026400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:137004800-137026400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:137005000-137022600	Strong transcription	Brain Hippocampus Middle	brain
32	chr9:137005000-137022600	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr9:137005000-137023800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:137005000-137024000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:137005000-137024000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr9:137005000-137024000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr9:137005000-137024200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr9:137005000-137024400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr9:137005000-137024400	Strong transcription	Rectal Smooth Muscle	rectum
40	chr9:137005000-137024600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:137005000-137024600	Strong transcription	Thymus	Thymus
42	chr9:137005000-137025000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr9:137005000-137025000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr9:137005000-137025200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:137005000-137025400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:137005000-137025600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:137005000-137026200	Strong transcription	Placenta	Placenta
48	chr9:137005000-137026400	Strong transcription	Brain Germinal Matrix	brain
49	chr9:137005200-137023200	Strong transcription	Brain Anterior Caudate	brain
50	chr9:137005200-137024200	Strong transcription	Skeletal Muscle Male	skeletal muscle

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