Variant report

Variant	rs3733418
Chromosome Location	chr4:165878335-165878336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:165868972..165872041-chr4:165876298..165879460,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236941	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10007789	0.84[CHD][hapmap]
rs10517825	0.84[CHD][hapmap]
rs11100583	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11942693	0.90[CHB][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap]
rs11942750	0.90[CHB][hapmap]
rs12507869	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12510464	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12512234	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12647427	0.89[CHB][hapmap]
rs13110309	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13110766	0.85[TSI][hapmap]
rs13111010	0.81[TSI][hapmap]
rs13120990	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs13134940	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13137799	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs13144590	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13151290	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13151735	0.84[CHB][hapmap]
rs1401399	0.81[EUR][1000 genomes]
rs1401401	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17623445	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280325	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3733419	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3889248	0.91[CHD][hapmap];0.80[JPT][hapmap]
rs4690797	0.91[CEU][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4691138	0.91[CEU][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4691139	0.80[CHD][hapmap]
rs4691141	0.81[JPT][hapmap]
rs6834073	0.86[CHD][hapmap];0.80[JPT][hapmap]
rs71641138	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72697952	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7656863	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7657444	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7657639	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7693977	0.80[CHD][hapmap]
rs8180162	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9762579	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019150	chr4:165505585-165907924	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv880382	chr4:165793001-165964290	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	esv2757965	chr4:165801816-165976350	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv2759299	chr4:165801816-165976350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv528686	chr4:165814359-165930168	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv967697	chr4:165843736-165889668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1015970	chr4:165852926-165973078	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv830140	chr4:165855999-165956612	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv517554	chr4:165859951-165878335	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
15	esv2760876	chr4:165861386-165893486	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	esv20237	chr4:165861441-165883885	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
17	nsv10607	chr4:165861465-165886549	Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	esv3692850	chr4:165868229-165879381	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
19	esv2421831	chr4:165868229-165882293	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3733418	C4orf39	cis	parietal	SCAN
rs3733418	C4orf39	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165877200-165879000	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr4:165877400-165878800	Active TSS	Primary T cells from cord blood	blood
3	chr4:165877400-165879000	Active TSS	Stomach Smooth Muscle	stomach
4	chr4:165877600-165878400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:165877600-165878400	Active TSS	Fetal Stomach	stomach
6	chr4:165877600-165878600	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr4:165877600-165878600	Active TSS	Colon Smooth Muscle	Colon
8	chr4:165877600-165878800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr4:165877600-165878800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:165877600-165878800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:165877600-165878800	Active TSS	Fetal Brain Female	brain
12	chr4:165877600-165878800	Active TSS	Fetal Intestine Small	intestine
13	chr4:165877600-165879000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr4:165877600-165879000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:165877600-165879000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr4:165877600-165879000	Active TSS	A549	lung
17	chr4:165877600-165879200	Active TSS	NHDF-Ad	bronchial
18	chr4:165877600-165879400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr4:165877600-165879400	Active TSS	Brain Hippocampus Middle	brain
20	chr4:165877600-165879600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:165877600-165879600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:165877600-165879800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr4:165877600-165880000	Active TSS	Brain Germinal Matrix	brain
24	chr4:165877600-165880200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:165877600-165880200	Active TSS	HSMM	muscle
26	chr4:165877600-165880400	Active TSS	HSMMtube	muscle
27	chr4:165877800-165878400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr4:165877800-165878400	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr4:165877800-165878400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:165877800-165878400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:165877800-165878400	Active TSS	Thymus	Thymus
32	chr4:165877800-165878400	Active TSS	GM12878-XiMat	blood
33	chr4:165877800-165878400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr4:165877800-165878400	Active TSS	NH-A	brain
35	chr4:165877800-165878600	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr4:165877800-165878600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:165877800-165878600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:165877800-165878600	Flanking Bivalent TSS/Enh	Liver	Liver
39	chr4:165877800-165878600	Active TSS	Brain Angular Gyrus	brain
40	chr4:165877800-165878600	Active TSS	Colonic Mucosa	Colon
41	chr4:165877800-165878600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr4:165877800-165878600	Active TSS	Fetal Heart	heart
43	chr4:165877800-165878600	Flanking Active TSS	Lung	lung
44	chr4:165877800-165878600	Active TSS	Placenta Amnion	Placenta Amnion
45	chr4:165877800-165878600	Active TSS	Right Ventricle	heart
46	chr4:165877800-165878600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr4:165877800-165878600	Flanking Active TSS	HUVEC	blood vessel
48	chr4:165877800-165878800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:165877800-165878800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:165877800-165878800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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