Variant report

Variant	rs12309772
Chromosome Location	chr12:72742656-72742657
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10506654	1.00[CHB][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10735968	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs10879407	1.00[CHB][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10879408	0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11179165	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11179166	1.00[CHB][hapmap];0.91[YRI][hapmap]
rs11179167	1.00[CHB][hapmap];0.91[YRI][hapmap]
rs11179171	0.89[ASW][hapmap];1.00[CHB][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap]
rs11179178	1.00[CHB][hapmap];0.88[MKK][hapmap]
rs11179206	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11179209	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11179212	1.00[CHB][hapmap];0.81[LWK][hapmap];0.87[ASN][1000 genomes]
rs11179213	0.87[ASN][1000 genomes]
rs11179215	1.00[CHB][hapmap];0.81[LWK][hapmap];0.87[ASN][1000 genomes]
rs11179218	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11179220	0.87[ASN][1000 genomes]
rs12296702	1.00[CHB][hapmap]
rs12297838	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap]
rs12301142	0.87[ASN][1000 genomes]
rs12301315	1.00[CHB][hapmap];0.88[MKK][hapmap];0.87[ASN][1000 genomes]
rs12303037	0.87[ASN][1000 genomes]
rs12303303	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12304638	1.00[CHB][hapmap];0.92[YRI][hapmap]
rs12304721	1.00[CHB][hapmap];0.81[LWK][hapmap];0.87[ASN][1000 genomes]
rs12304897	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305426	1.00[CHB][hapmap];0.88[MKK][hapmap];0.87[ASN][1000 genomes]
rs12305656	1.00[CHB][hapmap]
rs12305935	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12306682	1.00[CHB][hapmap]
rs12308561	0.87[ASN][1000 genomes]
rs12311002	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12311242	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12311567	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12311646	1.00[CHB][hapmap];0.81[LWK][hapmap];0.87[ASN][1000 genomes]
rs12312988	0.87[ASN][1000 genomes]
rs12313587	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12313642	0.87[ASN][1000 genomes]
rs12318484	0.87[ASN][1000 genomes]
rs12322599	0.87[ASN][1000 genomes]
rs12425020	1.00[CHB][hapmap]
rs12425053	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12426300	1.00[ASN][1000 genomes]
rs1493843	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17111086	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs17111090	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap]
rs17111091	1.00[CHB][hapmap];0.92[YRI][hapmap]
rs17111098	0.89[ASW][hapmap];1.00[CHB][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap]
rs17111101	1.00[CHB][hapmap]
rs17111106	1.00[CHB][hapmap]
rs17111115	1.00[CHB][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs17111127	1.00[CHB][hapmap];0.88[MKK][hapmap];0.87[ASN][1000 genomes]
rs17111159	1.00[CHB][hapmap];0.81[LWK][hapmap];0.87[ASN][1000 genomes]
rs17111172	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17111173	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17111176	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17111190	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17111210	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1867507	0.87[ASN][1000 genomes]
rs56270780	0.87[ASN][1000 genomes]
rs61497936	0.87[ASN][1000 genomes]
rs7135873	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7137940	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs73344431	0.87[ASN][1000 genomes]
rs74104867	0.86[AFR][1000 genomes]
rs7961500	0.87[ASN][1000 genomes]
rs7966773	1.00[CHB][hapmap];0.88[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832452	chr12:72584971-72764495	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12309772	ZFC3H1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72740600-72746400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:72741800-72746600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links