Variant report

Variant	rs6552928
Chromosome Location	chr4:186769051-186769052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10213407	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1027525	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10866285	0.88[EUR][1000 genomes]
rs11132356	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11934426	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11934935	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11940307	0.94[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];0.95[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];1.00[ASN][1000 genomes]
rs13104167	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1869623	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1960151	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2133377	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2173478	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2310366	1.00[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2603734	0.83[EUR][1000 genomes]
rs2603735	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2648116	0.84[TSI][hapmap]
rs2648120	1.00[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2648122	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2648123	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3796646	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5006592	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56223023	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6833174	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833975	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834169	0.90[EUR][1000 genomes]
rs6835880	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6846833	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6848278	1.00[CEU][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7658732	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7660468	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7682191	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7693173	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1023917	chr4:186533075-186997806	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537420	chr4:186533075-186997806	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv830171	chr4:186610113-186789271	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv427702	chr4:186618031-186782377	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv530178	chr4:186659940-187478310	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1015236	chr4:186696172-187004074	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:186761200-186778400	Weak transcription	Aorta	Aorta
2	chr4:186767600-186769400	Enhancers	NHEK	skin
3	chr4:186767800-186769200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:186767800-186769200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:186767800-186769200	Enhancers	HMEC	breast
6	chr4:186767800-186769200	Enhancers	NHLF	lung
7	chr4:186767800-186769400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:186767800-186769400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:186767800-186769400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:186767800-186769400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:186767800-186769400	Enhancers	Fetal Muscle Leg	muscle
12	chr4:186768400-186769200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:186768400-186769200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:186768400-186769200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr4:186768400-186769200	Flanking Active TSS	HSMM	muscle
16	chr4:186768400-186769200	Flanking Active TSS	Osteobl	bone
17	chr4:186768400-186769400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr4:186768400-186769400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:186768400-186769400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr4:186768400-186769400	Enhancers	Placenta	Placenta
21	chr4:186768400-186769400	Flanking Active TSS	HSMMtube	muscle
22	chr4:186768400-186769600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr4:186768600-186769200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr4:186768600-186769200	Flanking Active TSS	A549	lung
25	chr4:186768600-186769200	Flanking Active TSS	Hela-S3	cervix
26	chr4:186768600-186769400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr4:186768600-186769400	Enhancers	H9 Cell Line	embryonic stem cell
28	chr4:186768600-186769400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr4:186768600-186769400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:186768600-186769400	Enhancers	Right Ventricle	heart
31	chr4:186768600-186769400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr4:186768600-186769600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:186768600-186769600	Enhancers	Right Atrium	heart
34	chr4:186768600-186770000	Enhancers	Left Ventricle	heart
35	chr4:186768600-186772200	Enhancers	Fetal Brain Male	brain
36	chr4:186768800-186769200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:186768800-186769200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr4:186768800-186769200	Flanking Active TSS	Fetal Heart	heart
39	chr4:186768800-186769200	Enhancers	Fetal Muscle Trunk	muscle
40	chr4:186768800-186769200	Enhancers	Psoas Muscle	Psoas
41	chr4:186768800-186769400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:186768800-186769400	Enhancers	HepG2	liver
43	chr4:186768800-186769400	Enhancers	NHDF-Ad	bronchial
44	chr4:186769000-186769200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:186769000-186769200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:186769000-186769200	Enhancers	NH-A	brain
47	chr4:186769000-186769400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr4:186769000-186769400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:186769000-186769600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:186769000-186770200	Weak transcription	Adipose Nuclei	Adipose

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