Variant report

Variant	rs4647376
Chromosome Location	chr9:98059856-98059857
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	chr9:98059172..98061613-chr9:98077027..98078592,2	MCF-7	breast:
2	chr9:98058741..98060444-chr9:98067413..98069103,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs171417	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs184818	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs2282216	0.81[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs356666	0.95[JPT][hapmap]
rs356669	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs356673	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs356675	0.95[JPT][hapmap]
rs356677	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs356678	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs356680	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs356684	0.95[JPT][hapmap]
rs356689	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs3780567	0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs3824486	0.81[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap]
rs416792	0.95[JPT][hapmap]
rs4647534	0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap]
rs4744451	0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs540412	0.85[JPT][hapmap]
rs565293	0.95[JPT][hapmap]
rs657637	0.81[JPT][hapmap]
rs7019043	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs944934	0.85[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4647376	NINJ1	cis	cerebellum	SCAN
rs4647376	AUH	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98046600-98063000	Weak transcription	Fetal Stomach	stomach
2	chr9:98050200-98067400	Weak transcription	A549	lung
3	chr9:98054800-98063000	Weak transcription	Lung	lung
4	chr9:98055000-98068600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:98055200-98065600	Weak transcription	Thymus	Thymus
6	chr9:98055400-98066000	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:98055600-98062000	Weak transcription	Aorta	Aorta
8	chr9:98058800-98061000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:98058800-98061400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:98059000-98060200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr9:98059000-98060400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:98059000-98060800	Enhancers	HepG2	liver
13	chr9:98059200-98060200	Enhancers	HSMM	muscle
14	chr9:98059200-98060800	Enhancers	HMEC	breast
15	chr9:98059200-98061800	Enhancers	Liver	Liver
16	chr9:98059400-98060000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:98059400-98060000	Enhancers	Small Intestine	intestine
18	chr9:98059400-98060400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:98059400-98060400	Enhancers	NHEK	skin
20	chr9:98059400-98060800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr9:98059400-98060800	Enhancers	Fetal Intestine Large	intestine
22	chr9:98059600-98060400	Enhancers	Fetal Intestine Small	intestine
23	chr9:98059600-98060600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:98059600-98063000	Weak transcription	Osteobl	bone
25	chr9:98059600-98067000	Weak transcription	GM12878-XiMat	blood
26	chr9:98059800-98063000	Weak transcription	NHLF	lung
27	chr9:98059800-98063200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:98059800-98064400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:98059800-98068000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:98059800-98068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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