Variant report

Variant	rs1742868
Chromosome Location	chr14:36536949-36536950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr14:36536723-36537053	GM12892	blood:	n/a	n/a
2	YY1	chr14:36536752-36537072	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr14:36536758-36536997	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:36530186..36532965-chr14:36536832..36539253,2	K562	blood:

Variant related genes	Relation type
ENSG00000257826	TF binding region
LINC00609	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11156905	0.80[EUR][1000 genomes]
rs1333312	0.82[EUR][1000 genomes]
rs1742867	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1742869	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1742876	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1957313	0.82[CEU][hapmap]
rs1957314	0.82[CEU][hapmap]
rs2780312	0.82[CEU][hapmap]
rs2780313	0.88[CEU][hapmap];0.83[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs2780314	0.85[CEU][hapmap]
rs367883	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs368181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs368187	0.81[EUR][1000 genomes]
rs368772	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs371191	0.89[EUR][1000 genomes]
rs375095	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs394246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs395212	0.96[CEU][hapmap];0.96[GIH][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs395660	0.90[EUR][1000 genomes]
rs396043	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs398745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs408783	0.99[EUR][1000 genomes]
rs410546	0.99[EUR][1000 genomes]
rs429041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs448145	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs4981320	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6571735	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7145211	0.96[CEU][hapmap]
rs7145546	0.96[CEU][hapmap]
rs7147401	1.00[CEU][hapmap]
rs8003253	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8007617	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8008989	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8020453	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs847514	0.96[EUR][1000 genomes]
rs847516	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs860200	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051045	chr14:36116503-36764947	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv542038	chr14:36116503-36764947	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1051147	chr14:36413342-36562863	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1040256	chr14:36501452-37172046	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv542040	chr14:36501452-37172046	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1742868	RP11-116N8.4	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:36524200-36538200	Weak transcription	Brain Hippocampus Middle	brain
2	chr14:36531000-36538400	Weak transcription	Brain Substantia Nigra	brain
3	chr14:36531400-36538400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr14:36535400-36537000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr14:36535400-36537200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr14:36535400-36537400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr14:36535800-36537000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:36536400-36538000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:36536600-36537600	Weak transcription	HMEC	breast
10	chr14:36536600-36538200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr14:36536800-36537200	Weak transcription	NHEK	skin

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