Variant report

Variant	rs12338655
Chromosome Location	chr9:97061454-97061455
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97054703..97056976-chr9:97060174..97062566,2	MCF-7	breast:
2	chr9:97058485..97060275-chr9:97060350..97062263,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs16912862	0.85[ASN][1000 genomes]
rs1971396	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3118753	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3118754	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3118756	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3118761	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3118762	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131901	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131902	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131904	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131910	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59717415	0.88[ASN][1000 genomes]
rs6479533	0.84[ASN][1000 genomes]
rs6479534	0.84[ASN][1000 genomes]
rs7041842	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7857240	0.85[ASN][1000 genomes]
rs9409511	1.00[ASN][1000 genomes]
rs9409512	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409513	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409718	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9695176	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9696843	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12338655	RP11-307E17.8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97032400-97064600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:97036800-97062600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:97039200-97062600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:97039400-97067600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:97040000-97064600	Weak transcription	Brain Germinal Matrix	brain
6	chr9:97041200-97065400	Weak transcription	Small Intestine	intestine
7	chr9:97042600-97068400	Weak transcription	Fetal Brain Female	brain
8	chr9:97042800-97064000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:97042800-97064400	Weak transcription	Hela-S3	cervix
10	chr9:97043200-97062800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:97043200-97062800	Weak transcription	Brain Angular Gyrus	brain
12	chr9:97043200-97063000	Weak transcription	HMEC	breast
13	chr9:97043200-97064000	Weak transcription	Colonic Mucosa	Colon
14	chr9:97043200-97064400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:97043800-97066400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:97044000-97062600	Weak transcription	A549	lung
17	chr9:97046000-97063600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr9:97050600-97062600	Weak transcription	Right Atrium	heart
19	chr9:97050800-97064600	Weak transcription	Right Ventricle	heart
20	chr9:97052600-97064200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:97053800-97063400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr9:97055200-97064200	Weak transcription	HSMM	muscle
23	chr9:97055400-97064200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:97055600-97061600	Weak transcription	Ovary	ovary
25	chr9:97055600-97062200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:97055600-97062200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr9:97055600-97062200	Weak transcription	Spleen	Spleen
28	chr9:97055600-97062400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:97055600-97062400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:97055600-97062400	Weak transcription	Aorta	Aorta
31	chr9:97055600-97062400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:97055600-97062400	Weak transcription	Esophagus	oesophagus
33	chr9:97055600-97062600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:97055600-97063200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr9:97055600-97063800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr9:97055600-97064200	Weak transcription	Fetal Intestine Large	intestine
37	chr9:97055600-97064400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:97055600-97066600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:97055600-97067800	Weak transcription	HepG2	liver
40	chr9:97055600-97068000	Weak transcription	Pancreas	Pancrea
41	chr9:97055800-97062000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:97055800-97062400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr9:97055800-97062600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:97055800-97064400	Weak transcription	Lung	lung
45	chr9:97056000-97061600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr9:97056000-97064600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:97056200-97062000	Weak transcription	GM12878-XiMat	blood
48	chr9:97056200-97062400	Weak transcription	Fetal Intestine Small	intestine
49	chr9:97056200-97062600	Weak transcription	Fetal Muscle Leg	muscle
50	chr9:97056400-97062000	Weak transcription	Thymus	Thymus

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