Variant report

Variant	rs334040
Chromosome Location	chr2:179095185-179095186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179058400..179060836-chr2:179093623..179096247,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RBM45-9	chr2:179095153-179095240	NONHSAT075739

Variant related genes	Relation type
ENSG00000079156	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10197166	0.86[JPT][hapmap]
rs11887212	0.88[ASN][1000 genomes]
rs170791	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs186736	0.86[JPT][hapmap]
rs2366157	0.86[JPT][hapmap];0.81[MEX][hapmap]
rs333996	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs333999	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs334002	0.82[ASW][hapmap];0.81[JPT][hapmap]
rs334005	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs334006	0.88[ASN][1000 genomes]
rs334007	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs334010	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs334011	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs334013	0.81[JPT][hapmap]
rs334014	0.81[JPT][hapmap]
rs334017	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs334035	0.86[JPT][hapmap]
rs334037	0.80[JPT][hapmap]
rs334041	0.87[CEU][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs334042	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334043	0.87[CEU][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs334044	0.87[CEU][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs334045	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs334102	0.93[JPT][hapmap]
rs334103	0.93[JPT][hapmap]
rs334110	0.93[JPT][hapmap]
rs6433715	0.83[YRI][hapmap]
rs6719178	0.86[JPT][hapmap]
rs7581504	0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap]
rs9989738	0.81[JPT][hapmap]

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	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs334040	FKBP7	cis	parietal	SCAN
rs334040	LOC100130691	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179079000-179101200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr2:179088800-179095800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:179090800-179095800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:179091000-179106400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:179091200-179101200	Weak transcription	Psoas Muscle	Psoas
6	chr2:179091200-179115000	Weak transcription	Aorta	Aorta
7	chr2:179092200-179102400	Weak transcription	NHDF-Ad	bronchial
8	chr2:179092800-179098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:179093800-179096600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:179094200-179095400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:179094200-179095600	Enhancers	NHEK	skin
12	chr2:179094200-179096200	Enhancers	HMEC	breast
13	chr2:179094400-179095400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:179094400-179096000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:179094600-179095200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:179094600-179095200	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr2:179094600-179096000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:179094800-179095200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:179094800-179095200	Enhancers	Brain Hippocampus Middle	brain

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