Variant report

Variant	rs6889371
Chromosome Location	chr5:113808364-113808365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12515458	0.93[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12719181	0.99[EUR][1000 genomes]
rs13156054	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13156389	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1459782	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs1459789	0.99[EUR][1000 genomes]
rs1599176	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.99[EUR][1000 genomes]
rs17136666	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1841248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1975851	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2125772	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2125773	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.99[EUR][1000 genomes]
rs34484477	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34512774	0.99[EUR][1000 genomes]
rs35211026	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35641030	0.98[EUR][1000 genomes]
rs4466150	0.98[EUR][1000 genomes]
rs4705506	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs4705671	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6870038	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs7730205	0.93[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs898354	0.93[CEU][hapmap];0.98[EUR][1000 genomes]
rs977850	0.81[AMR][1000 genomes];0.82[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	nsv830451	chr5:113684301-113829833	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv882729	chr5:113743628-114497708	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv830452	chr5:113798617-113975228	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS	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
rs6889371	TSSK1B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:113793600-113812800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr5:113793800-113812800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:113794200-113808600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:113794200-113813400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:113797000-113809800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:113800200-113813600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:113800400-113811000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:113803200-113816000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:113803600-113808600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:113807000-113810800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:113807600-113809600	Enhancers	Liver	Liver
12	chr5:113807600-113811600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:113808000-113809200	Weak transcription	Adipose Nuclei	Adipose
14	chr5:113808200-113808600	Weak transcription	Pancreas	Pancrea

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