Variant report

Variant	rs3853183
Chromosome Location	chr4:76556792-76556793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76438650..76441575-chr4:76556052..76558649,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174796	Chromatin interaction
ENSG00000163743	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10009902	0.81[AMR][1000 genomes]
rs10014281	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]
rs10025315	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10028884	0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10029110	0.92[AMR][1000 genomes]
rs11097069	0.90[EUR][1000 genomes]
rs11097070	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]
rs11729258	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11736474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11737705	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13116639	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13118426	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13133699	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137468	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13138717	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13140908	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1464070	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1464071	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1546539	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1548175	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1553984	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]
rs1553986	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1828629	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1967495	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]
rs1967496	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]
rs226416	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2280095	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2869174	0.87[AMR][1000 genomes]
rs324682	0.87[AMR][1000 genomes]
rs324683	0.84[AMR][1000 genomes]
rs324685	0.92[AMR][1000 genomes]
rs324689	1.00[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap];0.92[AMR][1000 genomes]
rs324692	0.89[AMR][1000 genomes]
rs324695	0.82[CHB][hapmap];0.89[AMR][1000 genomes]
rs324707	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324708	0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324711	0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324715	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324716	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]
rs324717	0.81[CEU][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324718	0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324721	0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs324724	0.89[AMR][1000 genomes]
rs324725	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap];0.89[AMR][1000 genomes]
rs324737	0.92[AMR][1000 genomes]
rs3796473	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];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796485	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796488	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3853184	1.00[ASW][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3942252	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4337757	0.86[EUR][1000 genomes]
rs4349625	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs436611	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs443952	0.82[CHB][hapmap];0.92[AMR][1000 genomes]
rs4859403	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859537	0.90[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs4859542	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859543	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]
rs4859544	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859545	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859546	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859547	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859548	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]
rs4859550	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]
rs5020591	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6419115	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6531778	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6531841	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6531866	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6531867	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6531868	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6531889	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6531902	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6531903	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6826858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6827809	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6828365	0.81[EUR][1000 genomes]
rs6829402	0.86[EUR][1000 genomes]
rs6832912	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6835702	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6835819	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6842216	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6855321	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6858741	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72651313	0.83[AMR][1000 genomes]
rs7356270	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7356310	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7657871	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7659408	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7662940	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7672378	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7674063	0.94[AMR][1000 genomes]
rs7674328	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7677150	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[MEX][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7685459	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691385	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]
rs7691765	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7696241	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9942164	0.85[AMR][1000 genomes];0.81[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	nsv879495	chr4:76493256-76585823	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv1793652	chr4:76521217-76581775	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3853183	PPEF2	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76554400-76556800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:76556200-76559200	Weak transcription	HSMM	muscle
3	chr4:76556200-76567600	Weak transcription	Liver	Liver
4	chr4:76556200-76590000	Weak transcription	Small Intestine	intestine
5	chr4:76556400-76558200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:76556400-76558600	Weak transcription	HMEC	breast
7	chr4:76556400-76559600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:76556400-76562200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:76556400-76562400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:76556400-76562600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:76556400-76562800	Weak transcription	Aorta	Aorta
12	chr4:76556400-76565000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:76556400-76565200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:76556400-76565200	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:76556400-76565600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:76556400-76565600	Weak transcription	Fetal Stomach	stomach
17	chr4:76556400-76567000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:76556400-76567400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:76556400-76567400	Weak transcription	Placenta	Placenta
20	chr4:76556400-76567400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:76556400-76567800	Weak transcription	NHDF-Ad	bronchial
22	chr4:76556400-76568000	Weak transcription	Primary B cells from cord blood	blood
23	chr4:76556400-76568000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:76556400-76568000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:76556400-76568200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:76556400-76568600	Weak transcription	Adipose Nuclei	Adipose
27	chr4:76556400-76568600	Weak transcription	GM12878-XiMat	blood
28	chr4:76556400-76568600	Weak transcription	HUVEC	blood vessel
29	chr4:76556400-76568600	Weak transcription	Osteobl	bone
30	chr4:76556400-76568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:76556400-76568800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:76556400-76568800	Weak transcription	Thymus	Thymus
33	chr4:76556400-76568800	Weak transcription	NH-A	brain
34	chr4:76556400-76569000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr4:76556400-76569000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:76556400-76569000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:76556400-76569000	Weak transcription	Stomach Mucosa	stomach
38	chr4:76556400-76569800	Weak transcription	Psoas Muscle	Psoas
39	chr4:76556400-76570000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:76556400-76570000	Weak transcription	Fetal Brain Male	brain
41	chr4:76556400-76570200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:76556400-76570600	Weak transcription	Esophagus	oesophagus
43	chr4:76556400-76570600	Weak transcription	Lung	lung
44	chr4:76556400-76570600	Weak transcription	Ovary	ovary
45	chr4:76556400-76570600	Weak transcription	Spleen	Spleen
46	chr4:76556600-76556800	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr4:76556600-76556800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
48	chr4:76556600-76556800	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr4:76556600-76556800	Enhancers	Fetal Heart	heart
50	chr4:76556600-76557000	Enhancers	Brain Cingulate Gyrus	brain

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