Variant report

Variant	rs4407528
Chromosome Location	chr4:147253995-147253996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:147162002..147168172-chr4:147253902..147262824,27	MCF-7	breast:
2	chr4:147250783..147254830-chr4:147255041..147259510,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251010	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10012310	0.86[MEX][hapmap]
rs10017463	0.80[MEX][hapmap]
rs10023228	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11726594	0.86[MEX][hapmap]
rs13105153	0.86[MEX][hapmap]
rs13110748	0.86[MEX][hapmap]
rs13114641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13121951	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1352066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1352068	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1485950	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2244306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2356822	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2630276	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2630279	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2630283	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2630287	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2679122	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2679129	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2679133	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2679137	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2679138	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2679139	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2679152	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4092340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4103540	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4516736	0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes]
rs4835032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835300	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835310	0.86[MEX][hapmap]
rs6537412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537421	0.86[MEX][hapmap]
rs6852118	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6857518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670877	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7682719	0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap]
rs7686137	0.85[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap]
rs7691153	0.84[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs923165	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9308200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9784489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3451660	chr4:147225135-147271246	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3443192	chr4:147225234-147271217	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3468025	chr4:147225279-147271172	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3468026	chr4:147225279-147271172	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1033640	chr4:147232217-147531881	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4407528	OTUD4	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147208400-147254600	Weak transcription	Gastric	stomach
2	chr4:147208600-147254800	Weak transcription	Adipose Nuclei	Adipose
3	chr4:147212800-147264200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:147215600-147254800	Weak transcription	Primary T cells from cord blood	blood
5	chr4:147229600-147257400	Weak transcription	Ovary	ovary
6	chr4:147233000-147255000	Weak transcription	Aorta	Aorta
7	chr4:147233200-147254400	Weak transcription	GM12878-XiMat	blood
8	chr4:147241800-147255200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr4:147241800-147284800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:147242800-147255000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr4:147243000-147255000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:147243200-147254800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:147244200-147255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:147246200-147254800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:147246200-147255000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:147246400-147254000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:147247600-147255000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:147248800-147257200	Weak transcription	Fetal Intestine Large	intestine
19	chr4:147249800-147255400	Weak transcription	Small Intestine	intestine
20	chr4:147249800-147256000	Weak transcription	Lung	lung
21	chr4:147249800-147256400	Weak transcription	Left Ventricle	heart
22	chr4:147249800-147256600	Weak transcription	Esophagus	oesophagus
23	chr4:147250400-147254800	Weak transcription	HSMMtube	muscle
24	chr4:147250600-147255000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:147251400-147254600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:147251400-147254600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr4:147251800-147254600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:147251800-147254600	Weak transcription	HSMM	muscle
29	chr4:147252200-147254400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:147252200-147254400	Weak transcription	A549	lung
31	chr4:147252200-147254400	Weak transcription	Osteobl	bone
32	chr4:147252200-147254600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:147252200-147254600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:147252200-147254600	Weak transcription	NH-A	brain
35	chr4:147252200-147254600	Weak transcription	NHLF	lung
36	chr4:147252400-147254400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:147252400-147254600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:147252400-147254600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:147252400-147254600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:147252400-147254600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:147252400-147254600	Weak transcription	NHDF-Ad	bronchial
42	chr4:147252400-147256000	Weak transcription	Hela-S3	cervix
43	chr4:147252600-147254600	Weak transcription	HMEC	breast
44	chr4:147252600-147254600	Weak transcription	NHEK	skin
45	chr4:147252600-147256000	Weak transcription	Fetal Lung	lung
46	chr4:147252600-147256400	Weak transcription	HUVEC	blood vessel
47	chr4:147252800-147254400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr4:147252800-147256400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:147253800-147254000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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