Variant report

Variant	rs6499562
Chromosome Location	chr16:72162855-72162856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10400963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10492813	0.80[JPT][hapmap]
rs1050361	0.80[JPT][hapmap]
rs1050362	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1050363	0.85[JPT][hapmap]
rs10852511	0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs11075922	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11075924	0.85[JPT][hapmap]
rs11643192	0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs12325142	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12325266	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs12444701	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12445586	0.82[ASN][1000 genomes]
rs12449073	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12708926	0.82[ASN][1000 genomes]
rs12708927	0.82[ASN][1000 genomes]
rs12708928	0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12924413	0.80[JPT][hapmap]
rs12928732	0.86[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12929749	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12932845	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs12933838	0.83[ASN][1000 genomes]
rs13334151	0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs16973716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2070937	0.90[JPT][hapmap]
rs2070939	0.90[JPT][hapmap]
rs2072142	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2074626	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2074627	0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2240243	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2241411	0.86[GIH][hapmap];0.95[JPT][hapmap]
rs2241412	0.85[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2287997	0.83[ASN][1000 genomes]
rs2288000	0.85[JPT][hapmap]
rs2288002	0.90[JPT][hapmap]
rs2303285	0.80[JPT][hapmap]
rs2550035	0.80[JPT][hapmap]
rs2550868	0.90[JPT][hapmap]
rs28432692	0.83[ASN][1000 genomes]
rs2854956	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs34714490	0.83[ASN][1000 genomes]
rs35460163	0.83[ASN][1000 genomes]
rs3764311	0.80[JPT][hapmap]
rs3764312	0.80[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs3764314	0.80[JPT][hapmap]
rs3812984	0.85[JPT][hapmap]
rs3812986	0.90[JPT][hapmap]
rs3812987	0.81[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3844425	0.90[JPT][hapmap]
rs3852781	0.80[JPT][hapmap]
rs3852782	0.90[JPT][hapmap]
rs3852784	0.90[JPT][hapmap]
rs3902135	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs3909541	0.85[JPT][hapmap]
rs3909543	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4238964	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4788609	0.90[JPT][hapmap]
rs4788610	0.90[JPT][hapmap]
rs56960650	0.81[ASN][1000 genomes]
rs6416742	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6499559	0.83[ASN][1000 genomes]
rs6499560	0.83[ASN][1000 genomes]
rs6680	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7184169	0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs7188058	0.81[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs7190995	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7191127	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7192730	0.82[ASN][1000 genomes]
rs7192848	0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs7198572	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7201225	0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes]
rs7201643	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs7203426	0.90[JPT][hapmap]
rs7203821	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs7940	0.95[JPT][hapmap]
rs8044555	0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs8044868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8047377	0.85[ASN][1000 genomes]
rs8050238	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs8051882	0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs8052338	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8052408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8059378	0.81[ASN][1000 genomes]
rs8059437	0.86[GIH][hapmap];0.95[JPT][hapmap]
rs8060770	0.81[ASN][1000 genomes]
rs8061282	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs8061459	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9924964	0.89[JPT][hapmap]
rs9925763	0.85[ASN][1000 genomes]
rs9926156	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9926927	0.80[JPT][hapmap]
rs9927526	0.85[JPT][hapmap]
rs9928157	0.95[JPT][hapmap]
rs9932951	0.84[GIH][hapmap];0.95[JPT][hapmap]
rs9936642	0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes]
rs9941087	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6499562	DHX38	cis	multi-tissue	Pritchard
rs6499562	HP	cis	cerebellum	SCAN
rs6499562	FAM65A	cis	cerebellum	SCAN
rs6499562	DHODH	cis	cerebellum	SCAN
rs6499562	VPS4A	cis	cerebellum	SCAN
rs6499562	SLC7A6OS	cis	parietal	SCAN

Chromatin state (count:31 , 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	chr16:72147000-72164800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr16:72147000-72172200	Weak transcription	Dnd41	blood
4	chr16:72147400-72164800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:72147600-72165000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr16:72147800-72170000	Weak transcription	Thymus	Thymus
7	chr16:72159000-72163000	Weak transcription	Ovary	ovary
8	chr16:72159200-72165200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr16:72159400-72163400	Weak transcription	Fetal Brain Female	brain
10	chr16:72159400-72170200	Weak transcription	Fetal Stomach	stomach
11	chr16:72159600-72168000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr16:72159800-72163000	Weak transcription	Fetal Intestine Large	intestine
13	chr16:72159800-72169800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr16:72160000-72164800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr16:72160000-72172400	Weak transcription	Fetal Intestine Small	intestine
16	chr16:72160000-72173400	Weak transcription	Pancreas	Pancrea
17	chr16:72160400-72166400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr16:72160600-72164000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr16:72160600-72167800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr16:72160600-72171400	Weak transcription	HepG2	liver
21	chr16:72160600-72171600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr16:72162000-72163200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr16:72162000-72165600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr16:72162200-72163000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr16:72162200-72163200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr16:72162400-72163000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr16:72162400-72163200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr16:72162400-72163200	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr16:72162600-72164200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr16:72162800-72163000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:72162800-72163200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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