Variant report

Variant	rs7038659
Chromosome Location	chr9:110055689-110055690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110044182..110049393-chr9:110054071..110058486,10	MCF-7	breast:
2	chr9:110050203..110052215-chr9:110053888..110055858,2	K562	blood:
3	chr9:110054408..110057220-chr9:110063474..110066259,2	K562	blood:
4	chr9:110054445..110058128-chr9:110059472..110062917,7	K562	blood:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11573614	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11573622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11573628	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11573629	0.88[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11573648	0.88[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11573675	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11573691	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11573693	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11573695	0.94[EUR][1000 genomes]
rs11573732	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1805330	1.00[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs41555117	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58278531	0.94[EUR][1000 genomes]
rs67197321	0.96[EUR][1000 genomes]
rs72736111	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72736112	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72736117	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72736120	0.98[EUR][1000 genomes]
rs72736121	0.98[EUR][1000 genomes]
rs72736122	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72736180	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72736182	0.98[EUR][1000 genomes]
rs72736185	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72736186	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72736187	0.98[EUR][1000 genomes]
rs72736188	0.98[EUR][1000 genomes]
rs72736192	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72736196	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736198	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72738204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72738207	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72738211	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72738212	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72738213	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72738215	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72738216	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72738220	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72738224	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72738225	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72738229	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv519266	chr9:110049477-110085255	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110047600-110067200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:110048000-110056000	Weak transcription	Aorta	Aorta
3	chr9:110048000-110058400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr9:110048400-110058000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr9:110048600-110058000	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr9:110048800-110056800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr9:110048800-110058600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr9:110048800-110059200	Enhancers	HepG2	liver
9	chr9:110048800-110061000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr9:110048800-110067800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:110048800-110069600	Weak transcription	Fetal Brain Male	brain
12	chr9:110049000-110058800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:110049000-110061200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:110049000-110061400	Weak transcription	NH-A	brain
15	chr9:110049000-110063000	Enhancers	Liver	Liver
16	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:110049200-110059200	Weak transcription	Fetal Intestine Small	intestine
19	chr9:110049200-110067000	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:110049400-110067800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr9:110049800-110058000	Weak transcription	Stomach Mucosa	stomach
22	chr9:110050200-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:110051200-110058400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:110051200-110066000	Weak transcription	Fetal Intestine Large	intestine
25	chr9:110051200-110067000	Weak transcription	Thymus	Thymus
26	chr9:110051600-110079200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:110051800-110057600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr9:110052000-110056800	Weak transcription	Primary B cells from cord blood	blood
29	chr9:110052000-110066800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:110052200-110061200	Weak transcription	Dnd41	blood
31	chr9:110052600-110056600	Weak transcription	Esophagus	oesophagus
32	chr9:110052600-110056600	Weak transcription	Gastric	stomach
33	chr9:110052600-110063200	Weak transcription	Placenta	Placenta
34	chr9:110052600-110067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:110052600-110067000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:110052600-110068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:110052600-110068600	Weak transcription	Brain Germinal Matrix	brain
38	chr9:110052600-110068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:110052600-110069200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr9:110052800-110056200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:110052800-110056200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:110052800-110056600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr9:110052800-110056600	Weak transcription	Brain Anterior Caudate	brain
44	chr9:110052800-110057200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:110052800-110061200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr9:110052800-110066000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:110053200-110056600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr9:110053400-110056000	Weak transcription	Brain Angular Gyrus	brain
49	chr9:110053400-110068600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr9:110053600-110056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links