Variant report

Variant	rs324716
Chromosome Location	chr4:76688888-76688889
allele	A/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	POLR2A	chr4:76688786-76688977	ProgFib	skin:	n/a	n/a

Variant related genes	Relation type
USO1	TF binding region

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

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10009902	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10010519	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10014281	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];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10025315	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10028884	0.83[CEU][hapmap];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]
rs10029110	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11097070	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11729258	0.91[CEU][hapmap];0.82[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11736474	0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13116639	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13118426	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13119659	0.88[ASN][1000 genomes]
rs13133699	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13137468	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13138717	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1546539	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1548175	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1553984	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1553986	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17220803	1.00[ASW][hapmap]
rs1967495	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1967496	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs226416	1.00[CEU][hapmap];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]
rs2280095	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2869174	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs324682	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs324683	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs324685	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324689	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];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324692	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324707	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324711	1.00[CEU][hapmap];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]
rs324715	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324721	1.00[CEU][hapmap];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]
rs324724	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324737	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34385808	0.84[EUR][1000 genomes]
rs3796473	0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3796485	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3853183	1.00[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3853184	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];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3942252	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4349625	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs436611	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859403	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4859542	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4859543	0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4859544	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4859545	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4859546	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4859547	0.91[CHD][hapmap];0.81[GIH][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4859548	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4859550	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]
rs5020591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6419115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531841	0.84[EUR][1000 genomes]
rs6531866	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6531867	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6531868	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6531889	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6531902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67474106	0.82[EUR][1000 genomes]
rs6826858	0.82[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6827809	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6835702	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6835819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6842216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6855321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6855960	0.85[EUR][1000 genomes]
rs6858741	0.82[AMR][1000 genomes]
rs72651313	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7356270	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7356310	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7657871	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7659408	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7662940	0.83[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];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7672378	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7674063	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7674328	0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7677150	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];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7685459	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7691385	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]
rs7691765	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7696241	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7698393	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9942164	0.82[AMR][1000 genomes]

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	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
4	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs324716	PPEF2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76650800-76737800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:76652000-76696400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:76652400-76725000	Weak transcription	Hela-S3	cervix
4	chr4:76668400-76698600	Weak transcription	Fetal Brain Male	brain
5	chr4:76671000-76689400	Weak transcription	Fetal Heart	heart
6	chr4:76671000-76739400	Weak transcription	Stomach Mucosa	stomach
7	chr4:76671600-76707800	Weak transcription	Right Ventricle	heart
8	chr4:76672000-76692200	Weak transcription	Colonic Mucosa	Colon
9	chr4:76674800-76715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:76675000-76727400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:76675400-76695400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:76676000-76696400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:76676200-76689400	Weak transcription	NHLF	lung
14	chr4:76676200-76695200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:76676200-76695800	Weak transcription	Brain Substantia Nigra	brain
16	chr4:76676200-76696000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:76676400-76692000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:76676400-76695800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:76676400-76695800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:76676400-76696400	Weak transcription	Esophagus	oesophagus
21	chr4:76676400-76696400	Weak transcription	Pancreas	Pancrea
22	chr4:76676400-76696800	Weak transcription	NHEK	skin
23	chr4:76676400-76697200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:76676400-76704800	Weak transcription	Aorta	Aorta
25	chr4:76676400-76704800	Weak transcription	Gastric	stomach
26	chr4:76676400-76730600	Weak transcription	Spleen	Spleen
27	chr4:76676600-76692000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:76676600-76695800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:76676600-76695800	Weak transcription	Fetal Kidney	kidney
30	chr4:76676800-76689600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:76676800-76690200	Weak transcription	Small Intestine	intestine
32	chr4:76676800-76691600	Weak transcription	HMEC	breast
33	chr4:76676800-76691800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:76676800-76692000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:76676800-76692400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:76676800-76692400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:76676800-76695200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:76676800-76695400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:76676800-76695400	Weak transcription	A549	lung
40	chr4:76676800-76695800	Weak transcription	Brain Germinal Matrix	brain
41	chr4:76676800-76695800	Weak transcription	Ovary	ovary
42	chr4:76676800-76695800	Weak transcription	Psoas Muscle	Psoas
43	chr4:76676800-76695800	Weak transcription	Thymus	Thymus
44	chr4:76676800-76696400	Weak transcription	Brain Angular Gyrus	brain
45	chr4:76676800-76698400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:76676800-76698400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr4:76677000-76689000	Weak transcription	Fetal Lung	lung
48	chr4:76677000-76689600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:76677000-76691600	Weak transcription	Dnd41	blood
50	chr4:76677000-76691600	Weak transcription	K562	blood

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