Variant report

Variant	rs12597011
Chromosome Location	chr16:71417763-71417764
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11075886	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11075887	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12373064	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12373108	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12595924	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12596074	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12597949	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12599948	0.81[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs34297868	0.91[ASN][1000 genomes]
rs34623821	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34659305	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34770624	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35060794	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35097873	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35886140	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36086613	0.80[ASN][1000 genomes]
rs3935259	0.80[ASN][1000 genomes]
rs4149497	0.82[MEX][hapmap];1.00[YRI][hapmap]
rs4412976	0.88[ASN][1000 genomes]
rs4488452	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4630548	0.90[ASN][1000 genomes]
rs57243109	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6499513	0.85[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs7187354	1.00[YRI][hapmap]
rs7196440	0.81[ASN][1000 genomes]
rs7203012	0.86[ASN][1000 genomes]
rs72789961	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72789969	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs746732	0.81[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs7498368	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8044561	1.00[YRI][hapmap]
rs9926110	1.00[YRI][hapmap]
rs9929629	0.91[ASN][1000 genomes]
rs9935618	0.91[ASN][1000 genomes]
rs9940982	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv1062426	chr16:71307180-71423400	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv572949	chr16:71352071-71426563	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3417792	chr16:71416447-71419521	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12597011	HYDIN	cis	parietal	SCAN
rs12597011	TERF2	cis	cerebellum	SCAN
rs12597011	HP	cis	parietal	SCAN
rs12597011	ELMO3	cis	parietal	SCAN
rs12597011	LRRC29	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71398800-71419800	Weak transcription	Brain Germinal Matrix	brain
2	chr16:71414600-71418400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:71416400-71419400	Strong transcription	Adipose Nuclei	Adipose
4	chr16:71416600-71417800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr16:71416600-71418400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr16:71416600-71419400	Enhancers	Esophagus	oesophagus
7	chr16:71416800-71417800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr16:71416800-71418000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr16:71416800-71420600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr16:71417200-71417800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr16:71417200-71418200	Enhancers	Fetal Brain Male	brain
12	chr16:71417400-71419000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr16:71417600-71417800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr16:71417600-71418400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr16:71417600-71420600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr16:71417600-71421200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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