Variant report

Variant	rs9936784
Chromosome Location	chr16:72230694-72230695
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72218659..72222633-chr16:72228772..72231216,3	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1006436	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10400963	0.86[JPT][hapmap]
rs1050363	0.81[ASW][hapmap]
rs10852511	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs11075924	1.00[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11643192	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs12325266	0.90[JPT][hapmap]
rs12449073	0.86[JPT][hapmap]
rs12918956	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12930285	0.94[ASN][1000 genomes]
rs12932845	0.80[ASW][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12935266	0.81[EUR][1000 genomes]
rs16973716	0.81[JPT][hapmap]
rs2070937	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2070939	0.82[CHB][hapmap]
rs2241411	0.87[ASW][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2288000	0.82[CHB][hapmap]
rs2288002	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2550868	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3812984	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812986	0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs3844425	0.93[ASW][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3844426	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852782	0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs3852784	0.87[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3852786	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3852787	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3909541	0.87[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4238964	0.86[JPT][hapmap]
rs4788461	0.80[EUR][1000 genomes]
rs4788464	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4788609	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4788610	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs6499562	0.81[JPT][hapmap]
rs6499564	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7186155	0.82[EUR][1000 genomes]
rs7192848	0.90[JPT][hapmap]
rs7193559	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7200003	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7201225	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs7201643	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7203426	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs7203821	0.81[JPT][hapmap]
rs7940	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs8044868	0.81[JPT][hapmap]
rs8052338	0.86[JPT][hapmap]
rs8052408	0.81[JPT][hapmap]
rs8059437	0.80[ASW][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs8060770	0.81[EUR][1000 genomes]
rs9924964	0.89[CHB][hapmap]
rs9927526	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9928157	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9932951	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9936642	0.81[GIH][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking 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	27 gene(s)	inside rSNPs	diseases
7	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
8	nsv1059599	chr16:72219769-72342170	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1066473	chr16:72229094-72373598	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9936784	FAM65A	cis	cerebellum	SCAN
rs9936784	SLC12A4	cis	parietal	SCAN
rs9936784	HP	cis	multi-tissue	Pritchard
rs9936784	DHX38	cis	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72214800-72232800	Weak transcription	Pancreas	Pancrea
2	chr16:72222000-72235800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr16:72223000-72236400	Weak transcription	Primary B cells from cord blood	blood
4	chr16:72225800-72231600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr16:72226000-72231400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr16:72226000-72231400	Weak transcription	NHDF-Ad	bronchial
7	chr16:72228600-72231600	Enhancers	Fetal Brain Male	brain
8	chr16:72228600-72236600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr16:72228800-72236600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr16:72229200-72232800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr16:72229200-72234400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr16:72229200-72240200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr16:72229600-72232000	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr16:72229800-72231200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr16:72230000-72231000	Weak transcription	Fetal Lung	lung
16	chr16:72230000-72231800	Enhancers	Brain Substantia Nigra	brain
17	chr16:72230200-72231200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:72230200-72231600	Enhancers	Fetal Brain Female	brain
19	chr16:72230400-72232800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr16:72230600-72231600	Enhancers	Brain Angular Gyrus	brain
21	chr16:72230600-72232000	Enhancers	Brain Cingulate Gyrus	brain
22	chr16:72230600-72232200	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links