Variant report

Variant	rs10863121
Chromosome Location	chr12:86343834-86343835
allele	G/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:36)

rs_ID	r²[population]
rs10082857	0.84[AFR][1000 genomes]
rs10779220	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10779226	1.00[JPT][hapmap]
rs10863094	0.83[ASN][1000 genomes]
rs10863111	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10863112	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10863114	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10863124	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11117089	0.83[ASN][1000 genomes]
rs11117115	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11117118	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11117122	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11117129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11615948	1.00[CHD][hapmap]
rs12313658	0.88[CEU][hapmap]
rs12369468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12370270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17354637	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2897186	0.83[ASN][1000 genomes]
rs4143239	0.83[ASN][1000 genomes]
rs4919774	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61929394	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61929395	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61929399	0.83[ASN][1000 genomes]
rs61929421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61929424	0.83[ASN][1000 genomes]
rs61930913	0.83[ASN][1000 genomes]
rs7132262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7135154	0.83[ASN][1000 genomes]
rs7303256	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73176252	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73177142	0.83[ASN][1000 genomes]
rs7966131	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7972773	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7973694	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7975310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1797806	chr12:86198935-86425608	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv559667	chr12:86318004-86416212	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10863121	MGAT4C	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86343000-86344200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:86343000-86346200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:86343200-86344200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:86343200-86344600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:86343200-86345600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr12:86343200-86346600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr12:86343600-86344400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:86343600-86345800	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr12:86343600-86346600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr12:86343600-86348000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr12:86343600-86348200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr12:86343800-86347000	Enhancers	HUES48 Cell Line	embryonic stem cell

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