Variant report

Variant	rs979955
Chromosome Location	chr2:172527973-172527974
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172522935..172524881-chr2:172525131..172528057,2	K562	blood:
2	chr2:172522193..172524881-chr2:172526221..172528057,2	K562	blood:
3	chr2:172525954..172528530-chr2:172530857..172533373,2	MCF-7	breast:
4	chr2:172526794..172530696-chr2:172532860..172536577,3	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11673831	0.88[EUR][1000 genomes]
rs11675891	0.89[EUR][1000 genomes]
rs13016580	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs13017695	0.83[EUR][1000 genomes]
rs13021138	0.87[EUR][1000 genomes]
rs1554259	0.80[EUR][1000 genomes]
rs17427311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17427473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17499306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17499502	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17848721	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1996424	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2138349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2357062	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34108287	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34632749	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34962243	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35162284	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3770459	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs62184174	0.86[EUR][1000 genomes]
rs72889853	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv997638	chr2:172442205-172560406	Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs979955	MAP1D	cis	parietal	SCAN
rs979955	KLHL23	cis	cerebellum	SCAN
rs979955	SLC25A12	cis	parietal	SCAN
rs979955	SLC25A12	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172525000-172529000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:172525400-172529200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:172525600-172528800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:172526800-172529200	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:172527800-172528000	Enhancers	Brain Cingulate Gyrus	brain
6	chr2:172527800-172528000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr2:172527800-172530600	Enhancers	Fetal Lung	lung

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