Variant report

Variant	rs7691385
Chromosome Location	chr4:76648290-76648291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:76648049-76650778	SK-N-SH	brain:	n/a	n/a
2	MAZ	chr4:76648193-76650840	IMR90	lung:	n/a	chr4:76650419-76650429
3	JUND	chr4:76648169-76648330	K562	blood:	n/a	n/a
4	RAD21	chr4:76648222-76650845	SK-N-SH	brain:	n/a	n/a
5	CUX1	chr4:76648151-76648836	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:76646646..76648324-chr4:76652983..76654497,2	K562	blood:
2	chr4:76596286..76601002-chr4:76645864..76652581,23	K562	blood:
3	chr4:76527827..76530761-chr4:76647722..76649257,2	K562	blood:
4	chr4:76585902..76588334-chr4:76648159..76650846,2	MCF-7	breast:
5	chr4:76647935..76649552-chr4:76714127..76716514,2	K562	blood:
6	chr4:76596470..76600480-chr4:76647707..76650691,10	MCF-7	breast:
7	chr4:76595601..76600505-chr4:76645864..76652704,29	K562	blood:
8	chr4:76584918..76589893-chr4:76647342..76651400,4	K562	blood:
9	chr4:76595422..76600363-chr4:76647674..76651574,9	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USO1-3	chr4:76648053-76648661	NONHSAT096937

No data

Variant related genes	Relation type
USO1	TF binding region
ENSG00000138757	Chromatin interaction
ENSG00000201644	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10009902	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10010519	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10014281	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025315	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10028884	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10029110	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097069	0.81[EUR][1000 genomes]
rs11097070	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11729258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736474	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13116639	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13118426	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13133699	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13137468	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13138717	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1464071	0.81[CEU][hapmap]
rs1546539	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1548175	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1553984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1553986	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1967495	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1967496	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs226416	0.91[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280095	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869174	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs324682	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs324683	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs324685	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324689	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324692	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324695	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324707	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324708	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324711	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324715	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324716	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324717	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324718	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324721	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324724	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324725	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324737	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796473	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3796485	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3796488	0.81[CEU][hapmap]
rs3853183	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3853184	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3942252	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4349625	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs436611	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs443952	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859403	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859542	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4859543	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859544	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4859545	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4859546	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859547	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859548	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859550	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5020591	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6419115	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6531778	0.81[CEU][hapmap]
rs6531841	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6531866	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6531867	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6531868	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6531889	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531902	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6531903	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6826858	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6827809	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6832912	0.81[CEU][hapmap]
rs6835702	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6835819	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6842216	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6855321	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6855960	0.80[EUR][1000 genomes]
rs6858741	0.84[AMR][1000 genomes]
rs72651313	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7356270	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657871	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659408	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7662940	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];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672378	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7674063	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7674328	1.00[CHB][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7677150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685459	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7691765	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7696241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698393	0.86[EUR][1000 genomes]
rs9942164	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS 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
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7691385	PPEF2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76631000-76648800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:76636400-76648600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:76640800-76648400	Weak transcription	Placenta	Placenta
4	chr4:76640800-76648400	Weak transcription	Right Atrium	heart
5	chr4:76640800-76649200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:76640800-76649400	Weak transcription	Lung	lung
7	chr4:76641400-76648400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:76641400-76648400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:76641400-76648600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:76641400-76648800	Weak transcription	Right Ventricle	heart
11	chr4:76643000-76648400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:76643200-76648400	Weak transcription	Left Ventricle	heart
13	chr4:76644000-76649200	Weak transcription	Gastric	stomach
14	chr4:76644200-76648400	Weak transcription	Pancreas	Pancrea
15	chr4:76647000-76648400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr4:76647000-76648600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr4:76647000-76648600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr4:76647200-76648400	Enhancers	Primary hematopoietic stem cells	blood
19	chr4:76647200-76648400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr4:76647200-76648400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:76647200-76648600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr4:76647200-76648600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:76647200-76648800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:76647200-76649000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr4:76647400-76648600	Enhancers	Colon Smooth Muscle	Colon
26	chr4:76647400-76648600	Enhancers	Ovary	ovary
27	chr4:76647400-76648800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:76647400-76648800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr4:76647400-76648800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr4:76647400-76648800	Flanking Active TSS	GM12878-XiMat	blood
31	chr4:76647400-76649000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:76647400-76649000	Flanking Active TSS	K562	blood
33	chr4:76647400-76649200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr4:76647400-76652200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr4:76647400-76652600	Active TSS	H1 Cell Line	embryonic stem cell
36	chr4:76647600-76648400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:76647600-76648400	Enhancers	Primary T cells from cord blood	blood
38	chr4:76647600-76648400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:76647600-76648400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr4:76647600-76648600	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr4:76647600-76648800	Enhancers	Fetal Heart	heart
42	chr4:76647600-76649000	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr4:76647600-76651200	Active TSS	Fetal Muscle Trunk	muscle
44	chr4:76647600-76652000	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr4:76647600-76652200	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr4:76647800-76648400	Enhancers	Brain Angular Gyrus	brain
47	chr4:76647800-76648400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr4:76647800-76648400	Enhancers	Fetal Stomach	stomach
49	chr4:76647800-76648400	Enhancers	Rectal Smooth Muscle	rectum
50	chr4:76647800-76648600	Enhancers	Primary T cells fromperipheralblood	blood

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