Variant report

Variant	rs3844425
Chromosome Location	chr16:72194325-72194326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72188975..72191321-chr16:72191647..72194383,3	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1006436	0.83[ASN][1000 genomes]
rs10400963	0.95[JPT][hapmap]
rs10492813	0.81[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs10492814	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs1050361	0.81[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs1050362	0.81[YRI][hapmap]
rs1050363	0.87[ASW][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs10852511	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11075924	0.93[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11643192	0.90[JPT][hapmap]
rs12325142	0.81[YRI][hapmap]
rs12325266	0.90[JPT][hapmap]
rs12449073	0.95[JPT][hapmap];0.81[YRI][hapmap]
rs12708928	0.81[YRI][hapmap]
rs12918956	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12924413	0.81[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs12928365	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12928732	0.81[JPT][hapmap]
rs12930285	0.86[ASN][1000 genomes]
rs12932845	0.86[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs12935266	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs13334151	0.81[JPT][hapmap]
rs1465457	0.93[YRI][hapmap]
rs16973716	0.90[JPT][hapmap]
rs2070937	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2070939	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap]
rs2072141	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs2072142	0.81[YRI][hapmap]
rs2074626	0.81[YRI][hapmap]
rs2074627	0.81[YRI][hapmap]
rs217181	1.00[YRI][hapmap]
rs2240243	0.81[YRI][hapmap]
rs2241411	0.93[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2241412	0.86[YRI][hapmap]
rs2288000	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2288002	0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs2303285	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs2550035	0.81[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs2550038	0.81[CHB][hapmap];0.92[YRI][hapmap]
rs2550868	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs3764311	0.81[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs3764312	0.81[JPT][hapmap]
rs3764314	0.81[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs3812984	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3812986	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3844426	0.84[ASN][1000 genomes]
rs3852781	0.81[CHB][hapmap];0.80[JPT][hapmap];0.93[YRI][hapmap]
rs3852782	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3852784	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3852786	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3852787	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3902135	0.81[JPT][hapmap]
rs3909541	0.80[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3909542	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4238964	0.87[GIH][hapmap];0.95[JPT][hapmap]
rs4788461	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4788464	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4788609	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]
rs4788610	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6499562	0.90[JPT][hapmap]
rs6499563	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6499564	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7186155	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7188058	0.81[JPT][hapmap]
rs7190995	0.81[YRI][hapmap]
rs7191127	0.81[YRI][hapmap]
rs7192848	0.95[GIH][hapmap];0.90[JPT][hapmap]
rs7193559	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7197020	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7198572	0.81[JPT][hapmap]
rs7200003	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7201225	0.90[JPT][hapmap]
rs7201643	0.81[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs7203426	0.80[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7203821	0.81[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs7940	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8044868	0.90[JPT][hapmap]
rs8051882	0.86[YRI][hapmap]
rs8052338	0.95[JPT][hapmap]
rs8052408	0.90[JPT][hapmap]
rs8059437	0.86[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs8060770	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8062895	0.93[YRI][hapmap]
rs9924964	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs9926156	0.86[YRI][hapmap]
rs9926927	0.81[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs9927526	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9928157	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs9932951	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs9936642	0.90[JPT][hapmap]
rs9936784	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3844425	DHODH	cis	cerebellum	SCAN
rs3844425	HPR	cis	parietal	SCAN
rs3844425	DHX38	cis	Lymphoblastoid	GTEx
rs3844425	DHX38	cis	lymphoblastoid	seeQTL
rs3844425	FAM65A	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72193000-72195000	Enhancers	Fetal Lung	lung
2	chr16:72193800-72194400	Enhancers	Brain Germinal Matrix	brain
3	chr16:72194000-72198400	Weak transcription	Fetal Brain Female	brain
4	chr16:72194200-72194400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr16:72194200-72194400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr16:72194200-72194400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr16:72194200-72194400	Enhancers	Fetal Brain Male	brain

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