Variant report

Variant	rs3213422
Chromosome Location	chr16:72042682-72042683
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr16:72042250-72043024	K562	blood:	n/a	chr16:72042855-72042862
2	SP2	chr16:72042297-72042893	HepG2	liver:	n/a	chr16:72042585-72042594 chr16:72042581-72042596
3	CHD1	chr16:72042352-72042959	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:72042265-72042859	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr16:72042432-72042832	HepG2	liver:	n/a	n/a
6	CHD2	chr16:72042355-72042904	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr16:72042566-72042993	GM12891	blood:	n/a	n/a
8	POU2F2	chr16:72042244-72043077	GM12878	blood:	n/a	n/a
9	MAX	chr16:72042287-72042986	K562	blood:	n/a	chr16:72042855-72042862
10	USF1	chr16:72042277-72042694	H1-hESC	embryonic stem cell:	n/a	chr16:72042476-72042497
11	USF1	chr16:72042237-72043120	H1-hESC	embryonic stem cell:	n/a	chr16:72042476-72042497
12	SP1	chr16:72042142-72043007	A549	lung:	n/a	chr16:72042585-72042597 chr16:72042446-72042457 chr16:72042638-72042647
13	POLR2A	chr16:72042552-72042925	A549	lung:	n/a	n/a
14	EP300	chr16:72042653-72042865	GM12878	blood:	n/a	chr16:72042781-72042794
15	SP1	chr16:72042247-72042747	H1-hESC	embryonic stem cell:	n/a	chr16:72042585-72042597 chr16:72042446-72042457 chr16:72042638-72042647
16	CEBPB	chr16:72042522-72042998	GM12878	blood:	n/a	n/a
17	POLR2A	chr16:72042184-72043054	MCF10A-Er-Src	breast:	n/a	n/a
18	GABPA	chr16:72042235-72043099	SK-N-SH	brain:	n/a	chr16:72042477-72042491 chr16:72042480-72042489
19	EGR1	chr16:72042305-72042730	K562	blood:	n/a	chr16:72042443-72042457
20	POLR2A	chr16:72042308-72042873	H1-hESC	embryonic stem cell:	n/a	n/a
21	HDAC2	chr16:72042498-72042991	K562	blood:	n/a	n/a
22	FOXM1	chr16:72042140-72043035	GM12878	blood:	n/a	n/a
23	TAF1	chr16:72042110-72043143	A549	lung:	n/a	n/a
24	YY1	chr16:72042283-72043075	SK-N-SH	brain:	n/a	chr16:72042931-72042940
25	TCF3	chr16:72042571-72042853	GM12878	blood:	n/a	n/a
26	MAX	chr16:72042153-72043192	MCF-7	breast:	n/a	chr16:72042855-72042862
27	REST	chr16:72042540-72042890	A549	lung:	n/a	chr16:72042716-72042729 chr16:72042723-72042736
28	SIN3AK20	chr16:72042183-72043158	MCF-7	breast:	n/a	n/a
29	YY1	chr16:72042392-72043027	HepG2	liver:	n/a	chr16:72042931-72042940
30	CREB1	chr16:72042393-72042867	ECC-1	luminal epithelium:	n/a	n/a
31	ATF2	chr16:72042595-72042889	H1-hESC	embryonic stem cell:	n/a	n/a
32	MYC	chr16:72042232-72043078	NB4	blood:	n/a	chr16:72042855-72042862
33	TAF1	chr16:72042263-72042899	H1-hESC	embryonic stem cell:	n/a	n/a
34	BHLHE40	chr16:72042210-72043067	HepG2	liver:	n/a	chr16:72042476-72042497
35	IRF1	chr16:72042192-72043033	K562	blood:	n/a	chr16:72042459-72042473 chr16:72042585-72042599
36	PBX3	chr16:72042305-72042894	A549	lung:	n/a	n/a
37	GABPA	chr16:72042135-72043201	HL-60	blood:	n/a	chr16:72042477-72042491 chr16:72042480-72042489
38	TBP	chr16:72042206-72042973	Hela-S3	cervix:	n/a	n/a
39	SP1	chr16:72042199-72042864	K562	blood:	n/a	chr16:72042585-72042597 chr16:72042446-72042457 chr16:72042638-72042647
40	MYC	chr16:72042315-72043053	MCF-7	breast:	n/a	chr16:72042855-72042862
41	USF1	chr16:72042271-72042703	SK-N-SH	brain:	n/a	chr16:72042476-72042497
42	POLR2A	chr16:72042180-72043124	GM12878	blood:	n/a	n/a
43	BHLHE40	chr16:72042235-72043059	K562	blood:	n/a	chr16:72042476-72042497
44	CEBPD	chr16:72042309-72042957	HepG2	liver:	n/a	n/a
45	POLR2A	chr16:72042240-72042915	K562	blood:	n/a	n/a
46	POLR2A	chr16:72042293-72042957	HepG2	liver:	n/a	n/a
47	UBTF	chr16:72042236-72042979	K562	blood:	n/a	n/a
48	SP2	chr16:72042292-72042923	HepG2	liver:	n/a	chr16:72042585-72042594 chr16:72042581-72042596
49	ELK1	chr16:72042274-72042880	GM12878	blood:	n/a	n/a
50	POLR2A	chr16:72042253-72043029	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:72042016..72045516-chr16:72126835..72130601,4	K562	blood:
2	chr16:71927023..71929738-chr16:72042635..72044988,2	K562	blood:
3	chr16:72042306..72048206-chr16:72125753..72130155,8	MCF-7	breast:
4	chr16:71962634..71964492-chr16:72041229..72043764,2	MCF-7	breast:
5	chr16:71927888..71929610-chr16:72042486..72044051,2	MCF-7	breast:
6	chr16:72040983..72044286-chr16:72126039..72129128,5	MCF-7	breast:
7	chr16:71928144..71931559-chr16:72041567..72044276,4	MCF-7	breast:
8	chr16:71840992..71843295-chr16:72041440..72044182,2	K562	blood:
9	chr16:72041299..72042941-chr20:49409461..49412156,2	MCF-7	breast:
10	chr16:71841795..71843345-chr16:72041440..72043953,2	K562	blood:

Variant related genes	Relation type
DHODH	TF binding region
ATP5A1P3	TF binding region
ENSG00000263311	TF binding region
ENSG00000102984	Chromatin interaction
ENSG00000140829	Chromatin interaction
ENSG00000182149	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000263320	Chromatin interaction
ENSG00000140830	Chromatin interaction
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10048111	0.80[ASN][1000 genomes]
rs1035559	0.83[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs1035560	0.89[ASN][1000 genomes]
rs11642993	0.89[ASN][1000 genomes]
rs11648003	0.90[ASN][1000 genomes]
rs11864453	0.89[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12599952	0.81[ASN][1000 genomes]
rs12708928	0.81[CHD][hapmap]
rs12928732	0.90[YRI][hapmap]
rs13334151	0.93[YRI][hapmap]
rs2012817	0.85[ASN][1000 genomes]
rs2074627	0.81[CHD][hapmap]
rs2278027	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3213420	0.94[ASN][1000 genomes]
rs3812987	0.90[YRI][hapmap]
rs3902135	0.90[YRI][hapmap]
rs4788454	0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs4788597	0.89[ASW][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4788598	0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs4788600	0.88[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs7184169	0.93[YRI][hapmap]
rs7185215	0.91[ASN][1000 genomes]
rs7185407	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs7186207	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7188058	0.90[YRI][hapmap]
rs7195958	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7198572	0.86[YRI][hapmap]
rs7201491	0.89[ASN][1000 genomes]
rs752434	0.89[ASN][1000 genomes]
rs8044555	0.93[YRI][hapmap]
rs8051239	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8051882	0.81[CHD][hapmap]
rs929866	0.89[ASW][hapmap];0.91[CHD][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs9941087	0.93[YRI][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	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv906894	chr16:72013539-72046211	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	n/a
9	esv1843253	chr16:72042428-72059149	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3213422	HPR	cis	cerebellum	SCAN
rs3213422	HP	cis	parietal	SCAN
rs3213422	DHODH	cis	parietal	SCAN
rs3213422	DHODH	cis	cerebellum	SCAN
rs3213422	DHODH	cis	Artery Aorta	GTEx
rs3213422	DHODH	cis	brain	BrainEAC
rs3213422	DHODH	cis	Esophagus Muscularis	GTEx
rs3213422	HPR	cis	parietal	SCAN
rs3213422	DHODH	cis	Adipose Subcutaneous	GTEx
rs3213422	DHODH	cis	Artery Tibial	GTEx
rs3213422	DHODH	cis	Nerve Tibial	GTEx
rs3213422	DHX38	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72041800-72043200	Active TSS	Primary T cells from cord blood	blood
2	chr16:72042000-72042800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr16:72042000-72042800	Active TSS	Duodenum Mucosa	Duodenum
4	chr16:72042000-72042800	Active TSS	Thymus	Thymus
5	chr16:72042000-72042800	Active TSS	Monocytes-CD14+_RO01746	blood
6	chr16:72042000-72043000	Active TSS	Brain Anterior Caudate	brain
7	chr16:72042000-72043000	Active TSS	Brain Cingulate Gyrus	brain
8	chr16:72042000-72043000	Active TSS	Fetal Thymus	thymus
9	chr16:72042000-72043200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr16:72042000-72043200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr16:72042000-72043200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr16:72042000-72043200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:72042000-72043200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr16:72042000-72043200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr16:72042000-72043200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr16:72042000-72043200	Active TSS	Liver	Liver
17	chr16:72042000-72043200	Active TSS	Brain Hippocampus Middle	brain
18	chr16:72042000-72043200	Active TSS	Fetal Intestine Small	intestine
19	chr16:72042000-72043200	Active TSS	Right Atrium	heart
20	chr16:72042000-72043200	Active TSS	GM12878-XiMat	blood
21	chr16:72042000-72043200	Active TSS	NHEK	skin
22	chr16:72042000-72043400	Active TSS	Stomach Smooth Muscle	stomach
23	chr16:72042000-72043600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr16:72042000-72043600	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr16:72042000-72043600	Active TSS	A549	lung
26	chr16:72042000-72043600	Active TSS	K562	blood
27	chr16:72042000-72043800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr16:72042000-72043800	Active TSS	Hela-S3	cervix
29	chr16:72042000-72043800	Active TSS	HSMM	muscle
30	chr16:72042200-72042800	Active TSS	Primary B cells from cord blood	blood
31	chr16:72042200-72042800	Active TSS	Primary T cells fromperipheralblood	blood
32	chr16:72042200-72042800	Active TSS	Primary hematopoietic stem cells	blood
33	chr16:72042200-72042800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr16:72042200-72042800	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr16:72042200-72042800	Active TSS	Adipose Nuclei	Adipose
36	chr16:72042200-72042800	Active TSS	Fetal Muscle Trunk	muscle
37	chr16:72042200-72042800	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr16:72042200-72043000	Active TSS	Primary B cells from peripheral blood	blood
39	chr16:72042200-72043000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
40	chr16:72042200-72043000	Active TSS	Colon Smooth Muscle	Colon
41	chr16:72042200-72043000	Active TSS	Fetal Muscle Leg	muscle
42	chr16:72042200-72043200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr16:72042200-72043200	Active TSS	H1 Cell Line	embryonic stem cell
44	chr16:72042200-72043200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr16:72042200-72043200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr16:72042200-72043200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr16:72042200-72043200	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr16:72042200-72043200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:72042200-72043200	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr16:72042200-72043200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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