Variant report

Variant	rs334014
Chromosome Location	chr2:179120345-179120346
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	chr2:179114503..179117797-chr2:179118067..179122993,4	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs101266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10197166	0.80[JPT][hapmap]
rs10203420	0.82[EUR][1000 genomes]
rs11680778	0.80[EUR][1000 genomes]
rs12469658	0.83[EUR][1000 genomes]
rs12474257	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476671	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13400415	1.00[YRI][hapmap]
rs147180	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2366157	0.80[JPT][hapmap]
rs333992	0.94[JPT][hapmap]
rs333993	0.94[JPT][hapmap]
rs333995	0.93[JPT][hapmap]
rs333996	0.81[JPT][hapmap]
rs333997	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333998	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334000	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334001	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334002	1.00[JPT][hapmap]
rs334004	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334005	0.81[JPT][hapmap]
rs334007	0.81[JPT][hapmap]
rs334009	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs334013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334017	0.81[JPT][hapmap]
rs334035	0.80[JPT][hapmap]
rs334040	0.81[JPT][hapmap]
rs334042	0.81[JPT][hapmap]
rs334045	0.81[JPT][hapmap]
rs334604	0.81[JPT][hapmap]
rs334616	0.88[JPT][hapmap]
rs551368	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6719178	0.80[JPT][hapmap]
rs6756651	0.82[JPT][hapmap]
rs7419749	0.86[ASW][hapmap]
rs7599683	0.82[JPT][hapmap]
rs9288016	0.86[EUR][1000 genomes]
rs9288017	0.81[EUR][1000 genomes]
rs9989738	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	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
rs334014	LOC100130691	cis	cerebellum	SCAN
rs334014	LOC100128288	trans	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179105400-179120800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:179107800-179123000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:179111200-179137400	Weak transcription	Right Atrium	heart
4	chr2:179112400-179120400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:179116400-179120600	Weak transcription	Psoas Muscle	Psoas
6	chr2:179116600-179120600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:179116800-179120600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:179116800-179120800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:179116800-179120800	Weak transcription	K562	blood
10	chr2:179117000-179120600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:179117200-179120600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:179119400-179121000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:179119400-179121200	Enhancers	Brain Anterior Caudate	brain
14	chr2:179120200-179121600	Enhancers	Fetal Muscle Leg	muscle
15	chr2:179120200-179122000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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