Variant report

Variant	rs12685781
Chromosome Location	chr9:92761630-92761631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:92753705..92756579-chr9:92759778..92762031,2	MCF-7	breast:
2	chr9:92758301..92760371-chr9:92760953..92763123,2	MCF-7	breast:
3	chr9:92216749..92221414-chr9:92756839..92763409,10	MCF-7	breast:
4	chr9:92218340..92220049-chr9:92760293..92762561,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130222	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10116454	0.92[CEU][hapmap]
rs10991740	0.85[CEU][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10991742	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs10991751	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10991758	0.81[EUR][1000 genomes]
rs10991799	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs10991819	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10993742	0.82[EUR][1000 genomes]
rs10993743	0.82[EUR][1000 genomes]
rs12685019	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13299384	0.81[EUR][1000 genomes]
rs13301471	0.92[CEU][hapmap]
rs16906087	0.92[CEU][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs16906093	0.92[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs34473649	0.81[EUR][1000 genomes]
rs34954114	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4744002	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744025	0.81[EUR][1000 genomes]
rs4744027	0.81[EUR][1000 genomes]
rs4744499	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744515	0.80[EUR][1000 genomes]
rs62558472	0.82[EUR][1000 genomes]
rs62558473	0.82[EUR][1000 genomes]
rs662867	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7027794	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9650758	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12685781	C9orf153	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92753600-92765400	Enhancers	Fetal Intestine Large	intestine
2	chr9:92754000-92765400	Enhancers	Fetal Intestine Small	intestine
3	chr9:92755000-92762000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr9:92756000-92761800	Weak transcription	Brain Substantia Nigra	brain
5	chr9:92756200-92761800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:92757200-92761800	Weak transcription	Hela-S3	cervix
7	chr9:92757200-92762400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:92757400-92761800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:92757400-92770000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:92757600-92761800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:92757600-92762000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:92757600-92762200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:92757600-92764200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:92757600-92770000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:92757800-92762200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:92758000-92761800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:92758000-92762200	Weak transcription	Fetal Kidney	kidney
18	chr9:92758200-92761800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:92758200-92762200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:92758600-92761800	Enhancers	Stomach Mucosa	stomach
21	chr9:92758800-92761800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr9:92758800-92767600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:92759600-92761800	Weak transcription	HSMM	muscle
24	chr9:92760600-92762000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:92760600-92762000	Enhancers	NHDF-Ad	bronchial
26	chr9:92760800-92761800	Enhancers	Colonic Mucosa	Colon
27	chr9:92760800-92761800	Enhancers	Duodenum Mucosa	Duodenum
28	chr9:92760800-92762000	Enhancers	Colon Smooth Muscle	Colon
29	chr9:92760800-92762600	Enhancers	Esophagus	oesophagus
30	chr9:92760800-92766000	Enhancers	Fetal Brain Male	brain
31	chr9:92761000-92761800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:92761000-92762000	Enhancers	Primary B cells from cord blood	blood
33	chr9:92761000-92762000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr9:92761000-92762000	Enhancers	Brain Germinal Matrix	brain
35	chr9:92761000-92762200	Enhancers	Fetal Heart	heart
36	chr9:92761000-92762200	Enhancers	Fetal Lung	lung
37	chr9:92761000-92762600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr9:92761000-92762600	Enhancers	Pancreas	Pancrea
39	chr9:92761200-92761800	Enhancers	Primary B cells from peripheral blood	blood
40	chr9:92761200-92761800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr9:92761200-92761800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr9:92761200-92761800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr9:92761200-92761800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:92761200-92761800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr9:92761200-92761800	Enhancers	Rectal Smooth Muscle	rectum
46	chr9:92761200-92761800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr9:92761200-92761800	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr9:92761200-92762000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:92761200-92762000	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr9:92761200-92762000	Enhancers	Primary hematopoietic stem cells	blood

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