Variant report

Variant	rs1558142
Chromosome Location	chr12:2022411-2022412
allele	C/T
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:31)

rs_ID	r²[population]
rs10735005	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11062008	1.00[CHB][hapmap]
rs11062010	1.00[ASN][1000 genomes]
rs12368779	1.00[CHB][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs1558141	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17801032	1.00[CHB][hapmap]
rs1990232	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008352	1.00[ASN][1000 genomes]
rs2013064	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429155	1.00[CHB][hapmap]
rs2429158	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429159	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429164	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429167	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2429168	1.00[ASN][1000 genomes]
rs2429169	1.00[CHB][hapmap]
rs2429184	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470409	1.00[ASN][1000 genomes]
rs2470438	1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470439	1.00[CHB][hapmap]
rs2906892	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315910	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs758157	1.00[ASN][1000 genomes]
rs758158	1.00[CHB][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs8181666	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181681	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181786	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886939	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs886941	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[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	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1046388	chr12:1964846-2034887	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1043329	chr12:1986238-2034887	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv557000	chr12:2008548-2045640	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv898600	chr12:2020045-2056363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1558142	EFCAB4B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2018400-2024400	Weak transcription	Spleen	Spleen
2	chr12:2020400-2027000	Enhancers	Fetal Thymus	thymus
3	chr12:2020400-2027400	Enhancers	Fetal Muscle Leg	muscle
4	chr12:2020600-2026000	Enhancers	Fetal Muscle Trunk	muscle
5	chr12:2021600-2022800	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr12:2021800-2023200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:2021800-2024400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:2021800-2024400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:2021800-2027400	Weak transcription	Psoas Muscle	Psoas
10	chr12:2022200-2022600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:2022200-2024200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:2022400-2026200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:2022400-2027000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:2022400-2027600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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