Variant report

Variant	rs10809841
Chromosome Location	chr9:12777909-12777910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:12716514..12718700-chr9:12776478..12778096,2	MCF-7	breast:
2	chr9:12775994..12778011-chr9:12786037..12787743,2	K562	blood:
3	chr9:12776291..12778540-chr9:12858744..12861808,3	MCF-7	breast:
4	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
5	chr9:12776937..12779598-chr9:12883479..12885184,2	MCF-7	breast:
6	chr9:12777697..12781582-chr9:12805623..12809956,4	MCF-7	breast:
7	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235448	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10120667	0.89[EUR][1000 genomes]
rs10120695	0.89[EUR][1000 genomes]
rs10125581	0.83[ASN][1000 genomes]
rs10756411	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10756412	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10756413	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10809839	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10809840	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10809842	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10809843	0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs10960792	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1326800	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1359701	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147250	0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs2181817	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2382371	0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs7468492	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers 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 target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12774600-12778000	Active TSS	NHDF-Ad	bronchial
2	chr9:12774800-12778000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:12774800-12778000	Active TSS	Colon Smooth Muscle	Colon
4	chr9:12774800-12778000	Active TSS	Fetal Intestine Large	intestine
5	chr9:12774800-12778000	Active TSS	Rectal Smooth Muscle	rectum
6	chr9:12774800-12778000	Active TSS	NHEK	skin
7	chr9:12774800-12778200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:12774800-12778200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:12774800-12778200	Active TSS	Aorta	Aorta
10	chr9:12774800-12778200	Active TSS	Fetal Stomach	stomach
11	chr9:12774800-12778200	Active TSS	Right Atrium	heart
12	chr9:12774800-12778400	Active TSS	NHLF	lung
13	chr9:12774800-12779000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr9:12774800-12779000	Active TSS	Stomach Smooth Muscle	stomach
15	chr9:12775000-12779200	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr9:12775800-12779000	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr9:12776200-12778200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:12776200-12779200	ZNF genes & repeats	Fetal Brain Male	brain
19	chr9:12776400-12778400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:12776600-12778600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:12776600-12778600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr9:12776600-12778600	Flanking Active TSS	Hela-S3	cervix
23	chr9:12776600-12779200	Transcr. at gene 5' and 3'	Fetal Lung	lung
24	chr9:12776800-12778200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:12776800-12778200	Active TSS	Fetal Kidney	kidney
26	chr9:12776800-12778200	Active TSS	Placenta	Placenta
27	chr9:12776800-12784400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:12777000-12778000	Weak transcription	Pancreas	Pancrea
29	chr9:12777000-12778000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:12777000-12778000	Active TSS	HMEC	breast
31	chr9:12777000-12778000	Active TSS	HSMMtube	muscle
32	chr9:12777000-12778200	Active TSS	Fetal Muscle Leg	muscle
33	chr9:12777000-12778200	Weak transcription	Gastric	stomach
34	chr9:12777000-12778400	Active TSS	Liver	Liver
35	chr9:12777000-12778400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr9:12777000-12784000	Weak transcription	Stomach Mucosa	stomach
37	chr9:12777000-12784200	Weak transcription	Small Intestine	intestine
38	chr9:12777000-12784200	Weak transcription	K562	blood
39	chr9:12777000-12784400	Weak transcription	HUVEC	blood vessel
40	chr9:12777000-12784600	Weak transcription	Left Ventricle	heart
41	chr9:12777000-12784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr9:12777200-12778000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:12777200-12778000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr9:12777200-12778200	Enhancers	HSMM	muscle
45	chr9:12777200-12778400	Flanking Active TSS	Osteobl	bone
46	chr9:12777200-12784000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:12777400-12778000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:12777400-12778000	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:12777400-12778000	Weak transcription	Ovary	ovary
50	chr9:12777400-12778400	Weak transcription	Brain Angular Gyrus	brain

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