Variant report

Variant	rs3764310
Chromosome Location	chr16:72048332-72048333
allele	C/T
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	RCOR1	chr16:72047671-72048944	K562	blood:	n/a	n/a
2	GATA1	chr16:72047535-72048673	PBDE	blood:	n/a	chr16:72048022-72048038
3	NR2F2	chr16:72047603-72048347	K562	blood:	n/a	n/a
4	POLR2A	chr16:72048316-72048470	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr16:72048197-72048459	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr16:72047019-72048462	K562	blood:	n/a	n/a
7	POLR2A	chr16:72045322-72048851	PBDE	blood:	n/a	n/a
8	ELF1	chr16:72048202-72048502	K562	blood:	n/a	chr16:72048357-72048368 chr16:72048364-72048377
9	ZC3H11A	chr16:72048262-72048507	K562	blood:	n/a	n/a
10	POLR2A	chr16:72047940-72048425	MCF10A-Er-Src	breast:	n/a	n/a
11	MAX	chr16:72047651-72048373	K562	blood:	n/a	chr16:72047854-72047864
12	STAT3	chr16:72046993-72048500	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72047753..72049344-chr16:72049457..72051063,2	MCF-7	breast:
2	chr1:231002470..231005143-chr16:72046924..72048591,2	MCF-7	breast:

Variant related genes	Relation type
DHODH	TF binding region
ENSG00000119280	Chromatin interaction
ENSG00000102967	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10048144	0.95[ASN][1000 genomes]
rs1465457	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288002	0.81[CHD][hapmap]
rs2550868	0.83[CHD][hapmap]
rs2878404	0.94[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4788454	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs4788456	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4788597	0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs4788598	0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4788600	0.84[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs752434	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8048262	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8062895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929866	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs9932951	0.81[CHD][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3764310	DHODH	cis	parietal	SCAN
rs3764310	CCDC79	cis	parietal	SCAN
rs3764310	NAE1	cis	parietal	SCAN
rs3764310	HP	cis	multi-tissue	Pritchard
rs3764310	FBXL8	cis	parietal	SCAN
rs3764310	LRRC36	cis	parietal	SCAN
rs3764310	DHODH	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72043000-72049600	Weak transcription	Aorta	Aorta
2	chr16:72043000-72063000	Weak transcription	Small Intestine	intestine
3	chr16:72043200-72048600	Weak transcription	Primary B cells from cord blood	blood
4	chr16:72043200-72049200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr16:72043200-72049400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr16:72043200-72049400	Weak transcription	Brain Substantia Nigra	brain
7	chr16:72043200-72049400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr16:72043200-72049600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr16:72043200-72049600	Weak transcription	Fetal Kidney	kidney
10	chr16:72043200-72049800	Weak transcription	Gastric	stomach
11	chr16:72043200-72051000	Weak transcription	Fetal Lung	lung
12	chr16:72043200-72051800	Weak transcription	Fetal Thymus	thymus
13	chr16:72043200-72052200	Weak transcription	Brain Angular Gyrus	brain
14	chr16:72043200-72053400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr16:72043200-72054000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr16:72043200-72054600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr16:72043200-72054800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr16:72043200-72054800	Weak transcription	Pancreas	Pancrea
19	chr16:72043200-72055000	Weak transcription	Colon Smooth Muscle	Colon
20	chr16:72043200-72055200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr16:72043200-72055200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr16:72043200-72056400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:72043200-72056600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr16:72043200-72057400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr16:72043200-72057800	Weak transcription	NHDF-Ad	bronchial
26	chr16:72043200-72061200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr16:72043200-72062800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr16:72043200-72069800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr16:72043200-72069800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr16:72043400-72051000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:72043600-72050000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr16:72043600-72075200	Weak transcription	Fetal Brain Male	brain
33	chr16:72043800-72049200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr16:72043800-72051200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr16:72043800-72056800	Weak transcription	HSMM	muscle
36	chr16:72044000-72054800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:72044000-72057400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr16:72044400-72049800	Strong transcription	A549	lung
39	chr16:72045600-72053400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr16:72045600-72059400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr16:72045600-72060200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr16:72045600-72060400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr16:72045600-72060600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr16:72045600-72062200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr16:72045600-72062400	Strong transcription	Dnd41	blood
46	chr16:72045800-72052600	Strong transcription	Fetal Intestine Small	intestine
47	chr16:72045800-72060200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr16:72045800-72060400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr16:72045800-72060400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr16:72045800-72064200	Strong transcription	Fetal Stomach	stomach

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