Variant report

Variant	rs12639930
Chromosome Location	chr4:100563550-100563551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:100560411..100562122-chr4:100562728..100564350,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10516445	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12641768	0.93[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12647188	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13105033	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13112253	0.86[CEU][hapmap]
rs13126189	0.95[ASN][1000 genomes]
rs13130949	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1352775	0.91[CEU][hapmap]
rs1491238	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2306985	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3805337	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3828543	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4699755	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6532825	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852647	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7659550	0.93[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7698798	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs881981	0.89[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs959247	0.93[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs991811	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv933074	chr4:100460951-100630600	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12639930	H2AFZ	cis	cerebellum	SCAN
rs12639930	ADH1B	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100553600-100564200	Weak transcription	Left Ventricle	heart
2	chr4:100553600-100564600	Weak transcription	Psoas Muscle	Psoas
3	chr4:100556400-100563800	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:100561800-100567400	Weak transcription	HSMMtube	muscle
5	chr4:100562400-100563800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:100562400-100563800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:100562400-100565000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:100563000-100563600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr4:100563000-100563800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:100563200-100564800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr4:100563400-100564400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:100563400-100564800	Enhancers	Fetal Heart	heart
13	chr4:100563400-100565000	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr4:100563400-100565200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
15	chr4:100563400-100565800	Enhancers	Adipose Nuclei	Adipose
16	chr4:100563400-100567000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr4:100563400-100567600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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