Variant report

Variant	rs1364063
Chromosome Location	chr16:69588572-69588573
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	chr16:69585478..69590758-chr16:69596695..69601394,7	MCF-7	breast:
2	chr16:69588513..69590779-chr16:69598119..69599753,2	K562	blood:

Variant related genes	Relation type
ENSG00000223109	Chromatin interaction
ENSG00000102908	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs11640319	0.83[ASW][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs11646575	0.80[AFR][1000 genomes]
rs12599391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12599637	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12923231	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12924052	0.89[YRI][hapmap]
rs12924872	0.84[EUR][1000 genomes]
rs12929503	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12933292	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13330951	0.90[JPT][hapmap];0.87[MEX][hapmap]
rs1437134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap]
rs1469908	0.82[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs2032912	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2161630	0.83[ASW][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.94[YRI][hapmap]
rs244415	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs244417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs244418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs244420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2917670	0.87[LWK][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap]
rs35967356	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848278	0.83[ASW][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs4633710	0.88[YRI][hapmap]
rs4783721	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4783722	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62052815	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62052816	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6499240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6499244	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs669696	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7187634	0.83[ASW][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs7191292	0.83[ASW][hapmap];0.92[LWK][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap]
rs7192380	0.83[ASW][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs7359336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap]
rs8049728	0.83[ASW][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs8055756	0.81[ASW][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs8061052	0.95[YRI][hapmap]
rs862320	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs889398	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs889399	0.96[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][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	nsv1852	chr16:69566121-69610962	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	17 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Menarche (age at onset)	25231870	GWAS catalog
Menarche (age at onset)	21102462	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1364063	AGRP	cis	cerebellum	SCAN
rs1364063	COG8	cis	cerebellum	SCAN
rs1364063	PDXDC2P	cis	parietal	SCAN
rs1364063	DUS2L	cis	cerebellum	SCAN
rs1364063	LCAT	cis	parietal	SCAN
rs1364063	HSF4	cis	cerebellum	SCAN
rs1364063	TPPP3	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69574600-69597800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:69587200-69589400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr16:69587600-69588600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr16:69587600-69588600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr16:69588200-69589800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr16:69588400-69588800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr16:69588400-69588800	Enhancers	K562	blood
8	chr16:69588400-69589600	Enhancers	Dnd41	blood
9	chr16:69588400-69589800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr16:69588400-69589800	Enhancers	Fetal Thymus	thymus
11	chr16:69588400-69590000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr16:69588400-69590000	Enhancers	Monocytes-CD14+_RO01746	blood

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