Variant report

Variant	rs484555
Chromosome Location	chr9:14085583-14085584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:14082992..14085963-chr9:14086167..14088394,2	MCF-7	breast:
2	chr9:14084490..14087404-chr9:14119723..14122409,2	K562	blood:
3	chr9:14081334..14082892-chr9:14085086..14086767,2	MCF-7	breast:
4	chr9:14084996..14087351-chr9:14092569..14095116,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10810093	0.81[GIH][hapmap]
rs497789	0.86[CHB][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap]
rs510777	0.81[EUR][1000 genomes]
rs574460	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs580845	0.83[GIH][hapmap]

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	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs484555	CCDC92	trans	parietal	SCAN
rs484555	C9orf93	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14073400-14092600	Weak transcription	Aorta	Aorta
2	chr9:14074800-14090400	Weak transcription	Adipose Nuclei	Adipose
3	chr9:14075400-14116000	Weak transcription	Gastric	stomach
4	chr9:14077800-14088800	Weak transcription	Fetal Brain Female	brain
5	chr9:14078000-14112800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr9:14078600-14088000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:14079800-14087800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:14079800-14094400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:14080000-14095400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:14080400-14086000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:14081200-14087000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:14081400-14096200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:14081400-14096400	Weak transcription	Brain Germinal Matrix	brain
14	chr9:14081400-14115800	Weak transcription	Hela-S3	cervix
15	chr9:14081600-14087000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:14081800-14087200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr9:14081800-14095600	Weak transcription	Fetal Brain Male	brain
18	chr9:14082000-14086800	Weak transcription	HSMM	muscle
19	chr9:14082000-14087000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:14082000-14090400	Weak transcription	Fetal Intestine Small	intestine
21	chr9:14082000-14096200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:14082000-14096200	Weak transcription	Osteobl	bone
23	chr9:14082200-14096000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:14082200-14096000	Weak transcription	HMEC	breast
25	chr9:14082400-14085800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:14082400-14096400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:14082400-14096600	Weak transcription	Liver	Liver
28	chr9:14082600-14092200	Weak transcription	NH-A	brain
29	chr9:14082600-14096000	Weak transcription	NHEK	skin
30	chr9:14083000-14092200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:14083000-14096200	Weak transcription	Ovary	ovary
32	chr9:14083400-14087800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:14083400-14096200	Weak transcription	Psoas Muscle	Psoas
34	chr9:14083400-14096400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr9:14083800-14096000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:14084200-14085800	Enhancers	Fetal Heart	heart
37	chr9:14084200-14089200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:14084400-14086000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:14084400-14090200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:14084600-14085800	Weak transcription	Fetal Lung	lung
41	chr9:14084600-14087600	Weak transcription	Fetal Stomach	stomach
42	chr9:14084600-14088200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr9:14084800-14087400	Strong transcription	HUVEC	blood vessel
44	chr9:14084800-14098600	Weak transcription	Pancreas	Pancrea
45	chr9:14085000-14094000	Weak transcription	A549	lung
46	chr9:14085200-14088200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:14085200-14092000	Weak transcription	Lung	lung
48	chr9:14085200-14096000	Weak transcription	Right Atrium	heart
49	chr9:14085400-14086000	Weak transcription	Fetal Muscle Leg	muscle
50	chr9:14085400-14087000	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links