Variant report

Variant	rs9739928
Chromosome Location	chr12:33148600-33148601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1032702	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1032703	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1032704	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10844411	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10844428	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11052385	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11052390	0.92[EUR][1000 genomes]
rs11052399	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052409	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11052413	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11608737	0.90[EUR][1000 genomes]
rs1353934	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353935	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500073	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1846638	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1909610	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1909611	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35969824	0.87[EUR][1000 genomes]
rs4318054	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4931672	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4931675	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6488115	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7295724	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7305797	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7305861	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306057	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7306202	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7315188	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7977438	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977579	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs904640	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9738114	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs985876	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs985877	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1054440	chr12:32872999-33150460	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv832367	chr12:33063644-33298967	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1039909	chr12:33132909-33244419	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1053849	chr12:33132909-33279169	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9739928	H3F3C	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:33140600-33164800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:33143000-33149800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:33143800-33150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:33144200-33150000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:33144400-33150000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:33147600-33150200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:33147600-33150200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:33147800-33149000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:33147800-33150200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:33148000-33149000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:33148000-33149000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:33148400-33148600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:33148400-33148800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:33148400-33149200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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