Variant report

Variant	rs3756187
Chromosome Location	chr4:8378332-8378333
allele	C/G
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	chr4:8378249-8378624	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr4:8377949-8378656	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr4:8377960-8378735	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr4:8377983-8378715	ECC-1	luminal epithelium:	n/a	chr4:8378703-8378710 chr4:8378325-8378333
5	MAX	chr4:8378052-8378569	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr4:8378083-8378689	ECC-1	luminal epithelium:	n/a	n/a
7	TEAD4	chr4:8378076-8378626	ECC-1	luminal epithelium:	n/a	n/a
8	TCF12	chr4:8378025-8378741	ECC-1	luminal epithelium:	n/a	chr4:8378703-8378710 chr4:8378325-8378333

Variant related genes	Relation type
ACOX3	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10030108	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719994	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2280572	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756188	0.83[ASN][1000 genomes]
rs735811	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs747580	0.82[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs747582	0.87[MEX][hapmap]
rs827006	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs827011	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs862345	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv878605	chr4:8332057-8378959	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv878607	chr4:8349738-8380857	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv878608	chr4:8349738-8386720	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv461219	chr4:8353829-8390646	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv593637	chr4:8353829-8390646	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv524994	chr4:8373832-8380857	Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
16	nsv878609	chr4:8373832-8407406	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv878610	chr4:8377058-8416976	ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3756187	ACOX3	cis	multi-tissue	Pritchard
rs3756187	MAN2B2	cis	parietal	SCAN
rs3756187	ACOX3	cis	lymphoblastoid	seeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8354600-8381000	Weak transcription	Right Atrium	heart
2	chr4:8355800-8384800	Weak transcription	Fetal Lung	lung
3	chr4:8360400-8394000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:8360400-8395600	Weak transcription	NHEK	skin
5	chr4:8362000-8395400	Weak transcription	Fetal Brain Male	brain
6	chr4:8362800-8380200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:8364000-8383400	Weak transcription	Colonic Mucosa	Colon
8	chr4:8364000-8388600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:8364200-8387000	Weak transcription	Dnd41	blood
10	chr4:8364800-8387000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:8364800-8392400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:8365000-8382800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:8365000-8385000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:8365200-8385000	Weak transcription	NHLF	lung
15	chr4:8365400-8383600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:8365600-8382200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:8365600-8388800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr4:8365800-8383600	Strong transcription	Fetal Stomach	stomach
19	chr4:8366000-8382800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:8366400-8378600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:8366400-8380600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:8366400-8411600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:8366800-8386000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:8366800-8390000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:8367400-8379200	Weak transcription	HSMMtube	muscle
26	chr4:8367400-8384800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr4:8367400-8386800	Weak transcription	Primary B cells from cord blood	blood
28	chr4:8367800-8384800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:8368000-8378800	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:8368000-8380600	Weak transcription	Thymus	Thymus
31	chr4:8368400-8379200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:8368400-8388400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:8368600-8380600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:8368800-8379600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:8368800-8382600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:8368800-8384200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:8368800-8386600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr4:8368800-8388800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:8371400-8383200	Strong transcription	Ovary	ovary
40	chr4:8371600-8383200	Strong transcription	Lung	lung
41	chr4:8372200-8387000	Strong transcription	Pancreas	Pancrea
42	chr4:8372600-8384000	Strong transcription	Placenta	Placenta
43	chr4:8372600-8389800	Strong transcription	Esophagus	oesophagus
44	chr4:8372800-8385000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:8373000-8385000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr4:8373000-8388200	Weak transcription	Osteobl	bone
47	chr4:8373200-8384800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr4:8373400-8401600	Strong transcription	Fetal Intestine Small	intestine
49	chr4:8373800-8379800	Weak transcription	Primary T cells from cord blood	blood
50	chr4:8374600-8381800	Strong transcription	Skeletal Muscle Male	skeletal muscle

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