Variant report

Variant	rs2780978
Chromosome Location	chr9:86239704-86239705
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86235893..86237501-chr9:86238448..86240518,2	MCF-7	breast:
2	chr9:86236280..86241962-chr9:86320992..86325340,9	MCF-7	breast:
3	chr9:86238599..86242233-chr9:86242446..86245459,4	K562	blood:
4	chr9:86153786..86156686-chr9:86238312..86239923,2	MCF-7	breast:
5	chr9:86236616..86242493-chr9:86533666..86537484,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165115	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1413293	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1572135	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1889260	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2780969	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2780972	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2780975	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2780977	0.84[ASN][1000 genomes]
rs2780979	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2780982	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2811899	0.84[AMR][1000 genomes]
rs2811900	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2811901	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2811902	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2811903	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2811905	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2811906	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2811909	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2811912	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2811919	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7018643	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv516587	chr9:86226119-86255765	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv3410885	chr9:86236957-86239705	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86238600-86265000	Weak transcription	Ovary	ovary
2	chr9:86238800-86241600	Flanking Active TSS	Fetal Thymus	thymus
3	chr9:86238800-86242200	Weak transcription	Gastric	stomach
4	chr9:86238800-86242800	Weak transcription	Esophagus	oesophagus
5	chr9:86238800-86243000	Weak transcription	Lung	lung
6	chr9:86238800-86243600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:86238800-86244400	Weak transcription	Aorta	Aorta
8	chr9:86238800-86246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:86238800-86246000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:86238800-86254600	Weak transcription	Left Ventricle	heart
11	chr9:86238800-86260600	Weak transcription	Right Ventricle	heart
12	chr9:86238800-86264600	Weak transcription	Psoas Muscle	Psoas
13	chr9:86239000-86240000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:86239000-86240000	Enhancers	Pancreas	Pancrea
15	chr9:86239000-86240200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:86239000-86240200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr9:86239000-86240400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr9:86239000-86240600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:86239000-86241400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:86239000-86241400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:86239000-86242200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:86239000-86244200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:86239000-86244200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:86239000-86244400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:86239000-86244400	Weak transcription	HSMM	muscle
26	chr9:86239000-86244600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:86239000-86244600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:86239000-86245200	Weak transcription	Fetal Kidney	kidney
29	chr9:86239000-86245400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:86239000-86250000	Weak transcription	HSMMtube	muscle
31	chr9:86239000-86264800	Weak transcription	HMEC	breast
32	chr9:86239000-86265200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:86239200-86240600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr9:86239200-86240600	Enhancers	K562	blood
35	chr9:86239200-86241200	Enhancers	Fetal Intestine Small	intestine
36	chr9:86239200-86241400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr9:86239200-86241600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:86239200-86241600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr9:86239200-86241600	Weak transcription	Fetal Stomach	stomach
40	chr9:86239200-86241600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:86239200-86241600	Flanking Active TSS	Thymus	Thymus
42	chr9:86239200-86241800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:86239200-86242000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr9:86239200-86242200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:86239200-86243000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr9:86239200-86243800	Weak transcription	A549	lung
47	chr9:86239200-86243800	Weak transcription	Osteobl	bone
48	chr9:86239200-86244000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr9:86239200-86244000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr9:86239200-86244000	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links