Variant report

Variant	rs4397503
Chromosome Location	chr9:12797896-12797897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:12784767..12786871-chr9:12796425..12798748,2	MCF-7	breast:
2	chr9:12793649..12798936-chr9:12813991..12818779,7	MCF-7	breast:
3	chr9:12774105..12776446-chr9:12796570..12799387,2	MCF-7	breast:
4	chr9:12773433..12781932-chr9:12782481..12798090,47	MCF-7	breast:
5	chr9:12775140..12777800-chr9:12796207..12799105,2	K562	blood:
6	chr9:12796888..12798629-chr9:12811320..12813907,2	MCF-7	breast:
7	chr9:12794123..12798425-chr9:12799018..12802796,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153714	Chromatin interaction
ENSG00000235448	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10122949	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10809846	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10960800	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10960803	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10960804	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10960805	0.85[EUR][1000 genomes]
rs10960808	0.88[EUR][1000 genomes]
rs10960813	0.81[EUR][1000 genomes]
rs1318454	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13289069	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34919266	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6474732	0.88[EUR][1000 genomes]
rs6474733	0.88[EUR][1000 genomes]
rs71474394	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71507332	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7859336	0.88[EUR][1000 genomes]
rs9298684	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs957224	0.84[AMR][1000 genomes];0.93[ASN][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	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
2	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
3	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
4	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
5	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
6	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
7	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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12785400-12808800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:12785800-12798200	Weak transcription	HSMMtube	muscle
3	chr9:12785800-12802200	Weak transcription	Left Ventricle	heart
4	chr9:12785800-12813600	Weak transcription	Fetal Intestine Large	intestine
5	chr9:12786000-12813600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr9:12786000-12813600	Weak transcription	Fetal Intestine Small	intestine
7	chr9:12786400-12798400	Weak transcription	Brain Hippocampus Middle	brain
8	chr9:12789200-12798600	Enhancers	NHDF-Ad	bronchial
9	chr9:12792000-12817200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:12792600-12798200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:12794400-12798600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:12794800-12811800	Weak transcription	Hela-S3	cervix
13	chr9:12795000-12809400	Weak transcription	HepG2	liver
14	chr9:12795800-12802200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:12795800-12813400	Weak transcription	Fetal Kidney	kidney
16	chr9:12795800-12813800	Weak transcription	Fetal Stomach	stomach
17	chr9:12796200-12798800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:12796400-12798600	Enhancers	A549	lung
19	chr9:12796600-12798600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:12796600-12799000	Enhancers	HMEC	breast
21	chr9:12796800-12799200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:12796800-12799400	Enhancers	NHEK	skin
23	chr9:12797000-12798200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr9:12797000-12799400	Enhancers	Fetal Lung	lung
25	chr9:12797200-12798400	Enhancers	Brain Substantia Nigra	brain
26	chr9:12797200-12798600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr9:12797200-12799200	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr9:12797200-12809200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:12797200-12809800	Weak transcription	Stomach Mucosa	stomach
30	chr9:12797400-12798000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:12797400-12798200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:12797400-12798600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:12797400-12801200	Weak transcription	NHLF	lung
34	chr9:12797600-12798000	Weak transcription	Colon Smooth Muscle	Colon
35	chr9:12797600-12798000	Weak transcription	Osteobl	bone
36	chr9:12797800-12798000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:12797800-12798600	Enhancers	Fetal Brain Female	brain

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