Variant report

Variant	rs6531866
Chromosome Location	chr4:76623379-76623380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10009902	0.81[EUR][1000 genomes]
rs10014281	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10025315	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10028884	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10029110	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11097069	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11097070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729258	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11736474	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11737705	0.84[EUR][1000 genomes]
rs13116639	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13118426	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133699	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13137468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140908	0.82[EUR][1000 genomes]
rs1464070	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1464071	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1546539	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1548175	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1553984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1553986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1828629	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1913299	0.82[AMR][1000 genomes]
rs1967495	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]
rs1967496	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]
rs226416	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2280095	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2869174	0.80[AMR][1000 genomes]
rs324682	0.80[AMR][1000 genomes]
rs324685	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324689	0.82[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324692	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324695	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324707	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs324708	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs324711	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs324715	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs324716	0.82[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs324717	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs324718	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs324721	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs324724	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324725	0.82[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs324737	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3796473	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796488	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3821977	0.84[ASN][1000 genomes]
rs3853183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3853184	0.82[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3942252	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4337757	0.82[EUR][1000 genomes]
rs4349625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436611	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs443952	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859403	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859537	0.91[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap]
rs4859542	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859543	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859544	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859547	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[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];0.97[ASN][1000 genomes]
rs4859548	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]
rs4859550	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5020591	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6419115	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6531778	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6531784	0.80[AMR][1000 genomes]
rs6531841	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531867	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531889	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6531902	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6531903	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6826858	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6827809	1.00[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6828365	0.84[EUR][1000 genomes]
rs6829402	0.82[EUR][1000 genomes]
rs6832912	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6835702	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6835819	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6842216	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6855321	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6858741	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7356270	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7356310	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7657871	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7659408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662940	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7672378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674063	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7674328	0.91[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7677150	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7685459	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7691385	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7691765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696241	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9942164	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][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
rs6531866	PPEF2	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76599200-76640000	Weak transcription	Aorta	Aorta
2	chr4:76599600-76623400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:76599600-76624000	Weak transcription	Brain Substantia Nigra	brain
4	chr4:76599600-76639800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:76599600-76639800	Weak transcription	Brain Angular Gyrus	brain
6	chr4:76599600-76639800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:76599600-76647600	Weak transcription	Fetal Brain Female	brain
8	chr4:76599800-76627800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:76600400-76640000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:76600600-76627000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:76605800-76623400	Weak transcription	K562	blood
12	chr4:76605800-76633200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:76607400-76640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:76613000-76623400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:76613200-76627800	Weak transcription	A549	lung
16	chr4:76613400-76623400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:76613800-76639000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:76613800-76639600	Weak transcription	Ovary	ovary
19	chr4:76614600-76630200	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:76614800-76628200	Weak transcription	Gastric	stomach
21	chr4:76615600-76639800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:76615600-76639800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:76615800-76639000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:76616000-76640000	Weak transcription	Lung	lung
25	chr4:76616200-76630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:76618200-76635000	Weak transcription	Adipose Nuclei	Adipose
27	chr4:76618400-76639000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:76618600-76623600	Weak transcription	Thymus	Thymus
29	chr4:76619000-76623600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:76619400-76633400	Weak transcription	Fetal Kidney	kidney
31	chr4:76619600-76630400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:76620000-76630400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:76620000-76640000	Weak transcription	Brain Germinal Matrix	brain
34	chr4:76620200-76623600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:76620200-76627600	Weak transcription	Liver	Liver
36	chr4:76620200-76627800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:76620200-76627800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:76620400-76627800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:76620400-76630400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:76620400-76630600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:76620400-76639600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:76620600-76623600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:76620600-76627600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:76620600-76627800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:76620600-76627800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:76620600-76628000	Weak transcription	Fetal Stomach	stomach
47	chr4:76620600-76631400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr4:76620600-76640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr4:76620800-76623400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:76620800-76630400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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