Variant report

Variant	rs12307410
Chromosome Location	chr12:106323568-106323569
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106320573..106324506-chr12:106327076..106328938,3	MCF-7	breast:
2	chr12:106322581..106324128-chr12:106531603..106533720,2	MCF-7	breast:
3	chr12:106322923..106333063-chr12:106528610..106534226,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000074590	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10507203	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10861526	0.85[EUR][1000 genomes]
rs10861527	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10861530	0.85[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs10861531	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112776	0.84[EUR][1000 genomes]
rs11112789	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112791	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11615749	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12301955	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12302909	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12367295	0.86[EUR][1000 genomes]
rs12368539	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12423582	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12426023	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1345544	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1345545	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1421441	0.85[CEU][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1421464	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1421467	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1541629	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17278606	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1862027	0.85[EUR][1000 genomes]
rs1862028	0.85[EUR][1000 genomes]
rs2374559	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2374561	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28635481	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4620812	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7133626	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7297930	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7300496	0.84[EUR][1000 genomes]
rs7300906	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7300926	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305359	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73387048	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7960296	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960880	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7964927	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7968454	0.84[EUR][1000 genomes]
rs7968564	0.85[EUR][1000 genomes]
rs7980152	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761768	chr12:106317265-106326204	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12307410	GLT8D2	cis	cerebellum	SCAN
rs12307410	CHST11	cis	parietal	SCAN
rs12307410	PAH	cis	parietal	SCAN
rs12307410	ARL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106314600-106324200	Weak transcription	Right Atrium	heart
2	chr12:106317000-106327600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:106317200-106324200	Weak transcription	Psoas Muscle	Psoas
4	chr12:106317200-106325800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:106321200-106327600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:106321800-106323600	Enhancers	HMEC	breast
7	chr12:106322000-106325400	Weak transcription	Esophagus	oesophagus
8	chr12:106322000-106325800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:106322200-106327600	Weak transcription	HSMM	muscle
10	chr12:106322600-106324200	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:106323000-106326200	Enhancers	Brain Germinal Matrix	brain
12	chr12:106323200-106325800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:106323200-106326800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:106323400-106324400	Weak transcription	HSMMtube	muscle
15	chr12:106323400-106324400	Weak transcription	NHEK	skin
16	chr12:106323400-106325200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:106323400-106325400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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