Variant report

Variant	rs4788609
Chromosome Location	chr16:72165986-72165987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72164371..72166445-chr16:72168033..72170206,2	K562	blood:
2	chr16:72125969..72129081-chr16:72163635..72166689,3	K562	blood:

Variant related genes	Relation type
ENSG00000140829	Chromatin interaction
ENSG00000140830	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10400963	0.95[JPT][hapmap];0.90[YRI][hapmap]
rs10492813	0.81[CHB][hapmap];0.80[JPT][hapmap];0.81[YRI][hapmap]
rs10492814	0.81[CHB][hapmap];0.81[YRI][hapmap]
rs1050361	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs1050363	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap]
rs10852511	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11075924	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11643192	0.90[JPT][hapmap]
rs12325266	0.90[JPT][hapmap]
rs12449073	0.95[JPT][hapmap]
rs12917999	0.82[EUR][1000 genomes]
rs12918956	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12924413	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs12928365	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12928732	0.81[JPT][hapmap]
rs12930702	0.88[EUR][1000 genomes]
rs12932845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12935266	0.96[CEU][hapmap];0.84[YRI][hapmap];0.94[EUR][1000 genomes]
rs13334151	0.82[JPT][hapmap]
rs16973716	0.90[JPT][hapmap]
rs2070937	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2070939	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2072141	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs217181	0.81[YRI][hapmap]
rs2241411	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2241412	0.81[YRI][hapmap]
rs2288000	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2288002	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2303285	0.80[JPT][hapmap];0.81[YRI][hapmap]
rs2550035	0.81[CHB][hapmap];0.80[JPT][hapmap];0.81[YRI][hapmap]
rs2550038	0.82[CHB][hapmap]
rs2550868	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3764311	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs3764312	0.81[JPT][hapmap]
rs3764314	0.81[CHB][hapmap];0.80[JPT][hapmap];0.81[YRI][hapmap]
rs3812984	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3812986	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3844425	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3852781	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3852782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3852784	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3852786	0.80[ASN][1000 genomes]
rs3890860	0.88[EUR][1000 genomes]
rs3902135	0.81[JPT][hapmap]
rs3909541	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3909542	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4238964	0.95[JPT][hapmap];0.81[YRI][hapmap]
rs4788458	0.82[EUR][1000 genomes]
rs4788461	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4788464	0.83[EUR][1000 genomes]
rs4788610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499557	0.82[EUR][1000 genomes]
rs6499562	0.90[JPT][hapmap]
rs6499563	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6499564	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7185840	0.87[EUR][1000 genomes]
rs7186155	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7188058	0.82[JPT][hapmap]
rs7188962	0.81[EUR][1000 genomes]
rs7189115	0.87[EUR][1000 genomes]
rs7189591	0.81[EUR][1000 genomes]
rs7190994	0.81[EUR][1000 genomes]
rs7192848	0.90[JPT][hapmap]
rs7197020	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7198572	0.81[JPT][hapmap]
rs7199261	0.80[EUR][1000 genomes]
rs7200003	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7200854	0.82[EUR][1000 genomes]
rs7201225	0.90[JPT][hapmap]
rs7201643	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs7201866	0.88[EUR][1000 genomes]
rs7202268	0.82[EUR][1000 genomes]
rs7203426	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs7203821	0.92[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs7940	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8044868	0.90[JPT][hapmap];0.88[YRI][hapmap]
rs8051882	0.81[YRI][hapmap]
rs8052338	0.95[JPT][hapmap]
rs8052408	0.90[JPT][hapmap]
rs8059437	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8060770	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8182213	0.81[EUR][1000 genomes]
rs9924964	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs9926156	0.89[YRI][hapmap]
rs9926927	0.81[CHB][hapmap];0.80[JPT][hapmap];0.81[YRI][hapmap]
rs9927526	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9928157	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9932951	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs9936642	0.90[JPT][hapmap]
rs9938382	0.80[EUR][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4788609	DHX38	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72146600-72166600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:72147000-72172200	Weak transcription	Dnd41	blood
3	chr16:72147800-72170000	Weak transcription	Thymus	Thymus
4	chr16:72159400-72170200	Weak transcription	Fetal Stomach	stomach
5	chr16:72159600-72168000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr16:72159800-72169800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr16:72160000-72172400	Weak transcription	Fetal Intestine Small	intestine
8	chr16:72160000-72173400	Weak transcription	Pancreas	Pancrea
9	chr16:72160400-72166400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr16:72160600-72167800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr16:72160600-72171400	Weak transcription	HepG2	liver
12	chr16:72160600-72171600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr16:72164400-72167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr16:72165400-72169200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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