Variant report

Variant	rs4859543
Chromosome Location	chr4:76608794-76608795
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76596307..76600318-chr4:76606592..76610261,3	K562	blood:
2	chr4:76600960..76603310-chr4:76607519..76610199,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138757	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

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

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv879497	chr4:76519096-76620803	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
rs4859543	PPEF2	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76599000-76619600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:76599000-76620400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:76599200-76620000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:76599200-76640000	Weak transcription	Aorta	Aorta
5	chr4:76599400-76613000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:76599400-76617400	Weak transcription	Fetal Stomach	stomach
7	chr4:76599400-76619200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:76599400-76620400	Weak transcription	Left Ventricle	heart
9	chr4:76599600-76610800	Weak transcription	Brain Anterior Caudate	brain
10	chr4:76599600-76611200	Weak transcription	HSMMtube	muscle
11	chr4:76599600-76611400	Weak transcription	HSMM	muscle
12	chr4:76599600-76612200	Weak transcription	Brain Germinal Matrix	brain
13	chr4:76599600-76615600	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:76599600-76621600	Weak transcription	Fetal Lung	lung
15	chr4:76599600-76623400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:76599600-76624000	Weak transcription	Brain Substantia Nigra	brain
17	chr4:76599600-76639800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:76599600-76639800	Weak transcription	Brain Angular Gyrus	brain
19	chr4:76599600-76639800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:76599600-76647600	Weak transcription	Fetal Brain Female	brain
21	chr4:76599800-76610800	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:76599800-76611800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:76599800-76612200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:76599800-76612600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:76599800-76612600	Weak transcription	A549	lung
26	chr4:76599800-76613000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:76599800-76613600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:76599800-76619800	Weak transcription	Liver	Liver
29	chr4:76599800-76621200	Weak transcription	HepG2	liver
30	chr4:76599800-76627800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr4:76600400-76640000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:76600600-76627000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:76600800-76612000	Weak transcription	Fetal Intestine Small	intestine
34	chr4:76603600-76612000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:76603600-76617600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:76604800-76612400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:76605200-76611000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:76605800-76612000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr4:76605800-76612200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:76605800-76623400	Weak transcription	K562	blood
41	chr4:76605800-76633200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:76606000-76610200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:76606000-76610400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:76606000-76619800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:76607400-76640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:76607600-76613800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr4:76607800-76609000	Enhancers	Primary T cells fromperipheralblood	blood
48	chr4:76607800-76609000	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr4:76607800-76609200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr4:76607800-76609200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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