Variant report

Variant	rs28440102
Chromosome Location	chr9:137009215-137009216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136931362..136933512-chr9:137005797..137009467,3	MCF-7	breast:
2	chr9:137009070..137011653-chr9:137013931..137016626,2	MCF-7	breast:
3	chr9:137008996..137010498-chr9:137011020..137012647,2	MCF-7	breast:
4	chr9:137009038..137010707-chr9:137020129..137022288,2	MCF-7	breast:
5	chr9:137006870..137008925-chr9:137009202..137011699,2	K562	blood:

Variant related genes	Relation type
ENSG00000169925	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]
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]
rs28705689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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: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	chr9:137003600-137024800	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr9:137004000-137017400	Strong transcription	HUVEC	blood vessel
5	chr9:137004000-137024000	Strong transcription	A549	lung
6	chr9:137004000-137024800	Strong transcription	Primary T cells from cord blood	blood
7	chr9:137004200-137015800	Weak transcription	Fetal Heart	heart
8	chr9:137004200-137016000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:137004200-137024400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:137004200-137024800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:137004200-137024800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr9:137004200-137025000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:137004200-137025000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:137004200-137026000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:137004400-137010800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:137004400-137011800	Weak transcription	Small Intestine	intestine
17	chr9:137004400-137013600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:137004400-137014200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:137004400-137024800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:137004400-137025800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr9:137004400-137025800	Strong transcription	Fetal Thymus	thymus
22	chr9:137004600-137010400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:137004600-137010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr9:137004600-137010800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:137004600-137011600	Strong transcription	HMEC	breast
26	chr9:137004600-137011600	Strong transcription	NHEK	skin
27	chr9:137004600-137015000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr9:137004600-137016200	Strong transcription	Spleen	Spleen
29	chr9:137004600-137024400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr9:137004600-137024600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr9:137004600-137024800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:137004600-137024800	Strong transcription	Gastric	stomach
33	chr9:137004600-137025000	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr9:137004600-137025000	Strong transcription	Dnd41	blood
35	chr9:137004600-137025800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:137004600-137026000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:137004600-137026200	Strong transcription	Fetal Intestine Large	intestine
38	chr9:137004600-137026200	Strong transcription	Hela-S3	cervix
39	chr9:137004600-137026400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:137004800-137009400	Strong transcription	HSMM	muscle
41	chr9:137004800-137024200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:137004800-137025000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr9:137004800-137025000	Strong transcription	Fetal Brain Female	brain
44	chr9:137004800-137025600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:137004800-137026400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:137004800-137026400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr9:137005000-137009800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr9:137005000-137010000	Strong transcription	Brain Substantia Nigra	brain
49	chr9:137005000-137010600	Strong transcription	Esophagus	oesophagus
50	chr9:137005000-137011200	Strong transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links