Variant report

Variant	rs4923964
Chromosome Location	chr15:44015080-44015081
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10163069	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11070411	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12443084	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12898584	0.82[EUR][1000 genomes]
rs12912881	0.81[EUR][1000 genomes]
rs17727853	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17795279	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2412821	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2729494	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2930529	0.87[EUR][1000 genomes]
rs2930530	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2930531	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3102448	0.83[EUR][1000 genomes]
rs3110081	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34681147	0.82[EUR][1000 genomes]
rs35105314	0.81[EUR][1000 genomes]
rs35333173	0.82[EUR][1000 genomes]
rs35822148	0.80[EUR][1000 genomes]
rs3844075	0.82[AFR][1000 genomes]
rs3862143	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3986209	0.93[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs495880	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs514311	0.95[CEU][hapmap]
rs528764	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs541871	0.95[CEU][hapmap]
rs56226333	0.83[EUR][1000 genomes]
rs56246169	0.82[EUR][1000 genomes]
rs56380203	0.82[EUR][1000 genomes]
rs62018900	0.82[EUR][1000 genomes]
rs62018940	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62018944	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6493090	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs654276	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs678084	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7174260	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7178230	0.93[EUR][1000 genomes]
rs8030536	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs8038068	1.00[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	esv2757598	chr15:43831923-44058634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv904150	chr15:43836478-44040965	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	esv2760393	chr15:43845422-44024490	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv904157	chr15:43852043-44019592	Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv904158	chr15:43852043-44053617	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv904163	chr15:43873489-44023963	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
13	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv904171	chr15:43895643-44016417	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv869676	chr15:43895704-44016490	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv1038991	chr15:43914737-44024490	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv1047213	chr15:43929339-44024490	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
18	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
19	nsv976928	chr15:43948866-44040886	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
20	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4923964	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44013400-44037400	Weak transcription	Fetal Intestine Small	intestine
2	chr15:44013800-44015400	Enhancers	Placenta	Placenta
3	chr15:44014200-44015800	Enhancers	Hela-S3	cervix
4	chr15:44015000-44015200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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