Variant report

Variant	rs7019989
Chromosome Location	chr9:102573112-102573113
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:102572742..102574801-chr9:102574988..102577297,2	MCF-7	breast:
2	chr9:102568407..102574196-chr9:102578455..102584967,12	MCF-7	breast:
3	chr9:102572497..102574101-chr9:102668923..102670528,2	MCF-7	breast:
4	chr9:102568851..102571702-chr9:102571875..102575192,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119508	Chromatin interaction
ENSG00000136874	Chromatin interaction
ENSG00000237461	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10156557	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988895	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10988898	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988904	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988905	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336436	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352835	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1405209	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526265	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16918734	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918008	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918009	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965564	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900222	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742773	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742774	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020207	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022059	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026022	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029504	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029559	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038780	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041475	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047636	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744685	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7467433	0.81[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	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893621	chr9:102342950-102585545	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv528025	chr9:102540386-102613672	Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv893622	chr9:102543355-102595685	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102547600-102573400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:102555400-102577200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:102557400-102581400	Weak transcription	Pancreas	Pancrea
4	chr9:102559800-102581600	Weak transcription	Gastric	stomach
5	chr9:102560000-102580600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:102560400-102580800	Weak transcription	Fetal Stomach	stomach
7	chr9:102561200-102573400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:102561200-102573400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr9:102561200-102580800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr9:102561600-102573600	Weak transcription	Aorta	Aorta
11	chr9:102562800-102580800	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:102562800-102580800	Weak transcription	HSMMtube	muscle
13	chr9:102563800-102577400	Weak transcription	Fetal Heart	heart
14	chr9:102564400-102577400	Weak transcription	Psoas Muscle	Psoas
15	chr9:102564400-102580000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:102564400-102581400	Weak transcription	Ovary	ovary
17	chr9:102564600-102573200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:102566000-102580800	Weak transcription	Left Ventricle	heart
19	chr9:102566600-102580800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr9:102567000-102573200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:102567200-102576800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:102567400-102581600	Weak transcription	Lung	lung
23	chr9:102570000-102573200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:102570000-102573200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr9:102570000-102573400	Weak transcription	GM12878-XiMat	blood
26	chr9:102570000-102576800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr9:102570000-102576800	Weak transcription	NHLF	lung
28	chr9:102570000-102580600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:102570000-102580800	Weak transcription	Liver	Liver
30	chr9:102570400-102580800	Weak transcription	Fetal Brain Female	brain
31	chr9:102570600-102579800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr9:102570600-102580600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:102570600-102580800	Weak transcription	Osteobl	bone
34	chr9:102570800-102580800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr9:102571000-102573200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr9:102571000-102577400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:102571200-102573200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:102571200-102580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:102571400-102574200	Strong transcription	Primary B cells from cord blood	blood
40	chr9:102571800-102573800	Enhancers	NHEK	skin
41	chr9:102571800-102576600	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr9:102572000-102574800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr9:102572000-102577800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr9:102572000-102577800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr9:102572200-102573400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr9:102572200-102574200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:102572200-102574800	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr9:102572400-102574200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr9:102572600-102573600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr9:102572600-102576800	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links