Variant report

Variant	rs12445586
Chromosome Location	chr16:72126276-72126277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:72126190-72126326	GM12878	blood:	n/a	n/a
2	MXI1	chr16:72126245-72128714	SK-N-SH	brain:	n/a	n/a
3	MAZ	chr16:72126160-72128982	IMR90	lung:	n/a	chr16:72127351-72127360

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:72117368..72119841-chr16:72123694..72126741,5	MCF-7	breast:
2	chr16:72087766..72090367-chr16:72125547..72128434,2	K562	blood:
3	chr16:72042306..72048206-chr16:72125753..72130155,8	MCF-7	breast:
4	chr16:72083527..72085440-chr16:72125131..72126986,2	MCF-7	breast:
5	chr16:72040983..72044286-chr16:72126039..72129128,5	MCF-7	breast:
6	chr16:72049013..72051278-chr16:72125940..72127742,2	MCF-7	breast:
7	chr16:72088867..72091285-chr16:72125547..72127887,2	K562	blood:
8	chr16:71840719..71844104-chr16:72124883..72128411,3	K562	blood:

No data

Variant related genes	Relation type
DHX38	TF binding region
ENSG00000261701	Chromatin interaction
ENSG00000260252	Chromatin interaction
ENSG00000166747	Chromatin interaction
ENSG00000102967	Chromatin interaction
ENSG00000257017	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10492813	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10492814	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1050361	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1050362	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075922	0.82[ASN][1000 genomes]
rs11862813	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12325142	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12444701	0.90[ASN][1000 genomes]
rs12445401	0.91[ASN][1000 genomes]
rs12448315	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12708925	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12708926	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12708927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12708928	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12924413	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12924886	0.88[ASN][1000 genomes]
rs12933838	0.80[ASN][1000 genomes]
rs16973716	0.83[ASN][1000 genomes]
rs2000999	0.88[ASN][1000 genomes]
rs2072141	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2072142	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074626	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074627	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240243	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241412	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269918	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2287997	0.95[ASN][1000 genomes]
rs2303285	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2550035	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2550038	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28432692	0.80[ASN][1000 genomes]
rs2854956	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34042070	0.86[ASN][1000 genomes]
rs34714490	0.81[ASN][1000 genomes]
rs35460163	0.81[ASN][1000 genomes]
rs3764311	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3764312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764314	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3794695	0.88[ASN][1000 genomes]
rs3812987	0.89[ASN][1000 genomes]
rs3852781	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3902135	0.81[ASN][1000 genomes]
rs5472	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6416742	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6499559	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499560	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6499561	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6499562	0.82[ASN][1000 genomes]
rs6680	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7184169	0.90[ASN][1000 genomes]
rs7188058	0.85[ASN][1000 genomes]
rs7190995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7191127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7194397	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7194668	0.80[ASN][1000 genomes]
rs7197453	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7197869	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7198572	0.81[ASN][1000 genomes]
rs8043606	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8044555	0.88[ASN][1000 genomes]
rs8044868	0.81[ASN][1000 genomes]
rs8047377	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8050238	0.89[ASN][1000 genomes]
rs8051882	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8052408	0.82[ASN][1000 genomes]
rs8058609	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8059378	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8061282	0.90[ASN][1000 genomes]
rs8061459	0.90[ASN][1000 genomes]
rs8062041	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9925763	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9926156	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9926927	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9932062	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9941087	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9941346	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	esv1808086	chr16:72088669-72128767	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a
10	esv3343168	chr16:72111500-72128436	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12445586	DHODH	cis	Artery Tibial	GTEx
rs12445586	DHX38	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72106600-72126400	Weak transcription	Small Intestine	intestine
2	chr16:72108000-72126400	Weak transcription	Fetal Heart	heart
3	chr16:72117000-72126600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:72119400-72126400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr16:72119400-72126400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr16:72120600-72126800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:72121800-72126400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr16:72123800-72126400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr16:72124200-72126400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr16:72124200-72126400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr16:72124200-72126400	Weak transcription	Fetal Kidney	kidney
12	chr16:72124400-72126400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr16:72124400-72126400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr16:72124400-72126400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr16:72124400-72126400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:72124400-72126400	Weak transcription	Aorta	Aorta
17	chr16:72124400-72126400	Weak transcription	Gastric	stomach
18	chr16:72124400-72126400	Weak transcription	Spleen	Spleen
19	chr16:72124600-72126400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr16:72124800-72126400	Weak transcription	HSMMtube	muscle
21	chr16:72125000-72126400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr16:72125000-72126400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr16:72125000-72126400	Enhancers	Brain Cingulate Gyrus	brain
24	chr16:72125000-72126400	Weak transcription	Colonic Mucosa	Colon
25	chr16:72125000-72126400	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr16:72125000-72126400	Enhancers	A549	lung
27	chr16:72125000-72126400	Weak transcription	NH-A	brain
28	chr16:72125000-72126600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr16:72125200-72126400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr16:72125200-72126400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr16:72125200-72126400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr16:72125200-72126400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr16:72125200-72126400	Enhancers	Brain Germinal Matrix	brain
34	chr16:72125200-72126400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr16:72125200-72126400	Enhancers	Rectal Smooth Muscle	rectum
36	chr16:72125200-72126600	Enhancers	Pancreas	Pancrea
37	chr16:72125200-72126800	Enhancers	Esophagus	oesophagus
38	chr16:72125400-72126400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr16:72125400-72126400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr16:72125400-72126400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr16:72125400-72126400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr16:72125400-72126400	Enhancers	Brain Hippocampus Middle	brain
43	chr16:72125400-72126400	Enhancers	Colon Smooth Muscle	Colon
44	chr16:72125400-72126400	Enhancers	Fetal Brain Male	brain
45	chr16:72125400-72126400	Enhancers	Fetal Intestine Small	intestine
46	chr16:72125400-72126400	Flanking Active TSS	HepG2	liver
47	chr16:72125400-72126800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:72125600-72126400	Enhancers	Primary T cells from cord blood	blood
49	chr16:72125600-72126400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr16:72125600-72126400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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