Variant report

Variant	rs3117604
Chromosome Location	chr4:74734668-74734669
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	POLR2A	chr4:74734477-74736814	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr4:74734603-74739143	HUVEC	blood vessel:	n/a	n/a
3	UBTF	chr4:74734594-74735423	K562	blood:	n/a	n/a
4	POLR2A	chr4:74734496-74739017	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr4:74734509-74738990	HUVEC	blood vessel:	n/a	n/a
6	ZBTB7A	chr4:74734596-74735138	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr4:74733614-74739431	MCF10A-Er-Src	breast:	n/a	n/a
8	IRF1	chr4:74734628-74734980	K562	blood:	n/a	n/a
9	TEAD4	chr4:74734353-74734903	K562	blood:	n/a	n/a
10	POLR2A	chr4:74734632-74734759	A549	lung:	n/a	n/a
11	RCOR1	chr4:74734468-74735351	K562	blood:	n/a	n/a
12	JUND	chr4:74734445-74734787	K562	blood:	n/a	n/a
13	POLR2A	chr4:74733612-74739638	MCF10A-Er-Src	breast:	n/a	n/a
14	MAZ	chr4:74734590-74735456	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:74719674..74726110-chr4:74728599..74734688,9	K562	blood:

Variant related genes	Relation type
CXCL1	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16850137	0.91[JPT][hapmap]
rs2115691	0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap]
rs2367291	0.87[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2886927	0.90[ASW][hapmap];0.87[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3097411	0.82[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs3097412	0.83[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[YRI][hapmap]
rs3111692	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3111694	0.90[ASW][hapmap];0.87[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3117597	0.90[CEU][hapmap];0.80[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3117598	0.90[ASW][hapmap];0.87[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3117600	0.87[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4074	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs516224	0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs58557052	0.81[AMR][1000 genomes]
rs6858086	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs9991272	0.83[CHD][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv432612	chr4:74723372-74774372	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3117604	NPFFR2	cis	parietal	SCAN
rs3117604	CXCL6	cis	parietal	SCAN
rs3117604	THAP6	cis	parietal	SCAN
rs3117604	SEPT11	cis	parietal	SCAN
rs3117604	G3BP2	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74733000-74735000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:74733600-74734800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr4:74733600-74738800	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr4:74733800-74736400	Active TSS	Rectal Smooth Muscle	rectum
5	chr4:74734000-74734800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:74734000-74734800	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr4:74734000-74734800	Flanking Active TSS	NHEK	skin
8	chr4:74734000-74735000	Flanking Active TSS	HUVEC	blood vessel
9	chr4:74734000-74735800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:74734000-74735800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:74734000-74736400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:74734200-74734800	Flanking Active TSS	K562	blood
13	chr4:74734200-74735000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
14	chr4:74734200-74735000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr4:74734200-74735400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr4:74734200-74735400	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr4:74734200-74735600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:74734200-74737000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:74734400-74734800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
20	chr4:74734400-74734800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
21	chr4:74734400-74734800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
22	chr4:74734400-74734800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:74734400-74734800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:74734400-74734800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:74734400-74734800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:74734400-74734800	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:74734400-74734800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
28	chr4:74734400-74734800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr4:74734400-74734800	Bivalent Enhancer	HepG2	liver
30	chr4:74734400-74734800	Flanking Active TSS	HMEC	breast
31	chr4:74734400-74734800	Flanking Bivalent TSS/Enh	NH-A	brain
32	chr4:74734400-74734800	Flanking Active TSS	NHDF-Ad	bronchial
33	chr4:74734400-74735000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:74734400-74735000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr4:74734400-74735000	Active TSS	Colonic Mucosa	Colon
36	chr4:74734400-74735000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
37	chr4:74734400-74735000	Flanking Active TSS	Osteobl	bone
38	chr4:74734400-74735200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
39	chr4:74734400-74735400	Bivalent/Poised TSS	Fetal Stomach	stomach
40	chr4:74734400-74735400	Active TSS	Thymus	Thymus
41	chr4:74734400-74735400	Active TSS	NHLF	lung
42	chr4:74734400-74735600	Flanking Active TSS	Liver	Liver
43	chr4:74734400-74735600	Active TSS	Colon Smooth Muscle	Colon
44	chr4:74734400-74735600	Bivalent Enhancer	Fetal Brain Male	brain
45	chr4:74734400-74735600	Active TSS	Placenta Amnion	Placenta Amnion
46	chr4:74734400-74735600	Active TSS	Stomach Mucosa	stomach
47	chr4:74734400-74735800	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr4:74734400-74735800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
49	chr4:74734400-74735800	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr4:74734400-74736200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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