Variant report

Variant	rs41431749
Chromosome Location	chr13:49208920-49208921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12584114	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584341	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584980	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12857866	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1326698	1.00[ASN][1000 genomes]
rs1575921	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17071937	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1926597	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2148515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3890505	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41487046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4151598	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4151613	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4334183	1.00[ASN][1000 genomes]
rs449268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7139763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7326934	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7338898	1.00[ASN][1000 genomes]
rs9316386	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9316387	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9316396	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9331984	1.00[CHB][hapmap]
rs9331994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332044	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332055	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332070	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9595914	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription 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 target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3495983	chr13:49181790-49222165	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3495984	chr13:49181790-49222165	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41431749	SIT1	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49201600-49210200	Weak transcription	Fetal Kidney	kidney
2	chr13:49202200-49210400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr13:49205000-49210400	Weak transcription	Stomach Mucosa	stomach
4	chr13:49207600-49210800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:49208600-49209400	ZNF genes & repeats	Dnd41	blood
6	chr13:49208800-49209000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr13:49208800-49209200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:49208800-49210400	Weak transcription	Adipose Nuclei	Adipose
9	chr13:49208800-49210800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:49208800-49213200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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