Variant report

Variant	rs6535572
Chromosome Location	chr4:148913738-148913739
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	chr4:148912653..148914620-chr4:148915114..148916621,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10021480	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10029825	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10519933	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317354	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13435037	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17024251	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28493775	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28552498	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28754881	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs36025358	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4364238	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs55912417	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56657155	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58201461	0.88[AMR][1000 genomes]
rs58357782	0.81[EUR][1000 genomes]
rs6535571	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6811259	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6849257	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6856135	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73854000	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs869762	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs869763	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9762680	0.82[ASN][1000 genomes]
rs9990586	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9996477	1.00[AMR][1000 genomes];0.88[ASN][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	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148866400-148927400	Weak transcription	Thymus	Thymus
2	chr4:148885600-148939000	Weak transcription	Pancreas	Pancrea
3	chr4:148886000-148917600	Weak transcription	Esophagus	oesophagus
4	chr4:148889200-148936200	Weak transcription	Fetal Intestine Large	intestine
5	chr4:148891600-148920600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:148891600-148928000	Weak transcription	A549	lung
7	chr4:148896600-148928400	Weak transcription	Spleen	Spleen
8	chr4:148897200-148917600	Weak transcription	Lung	lung
9	chr4:148898200-148920600	Weak transcription	NHEK	skin
10	chr4:148898200-148925400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:148903200-148914800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:148903400-148914600	Weak transcription	HSMMtube	muscle
13	chr4:148903400-148914800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:148903400-148915000	Weak transcription	Osteobl	bone
15	chr4:148905800-148918000	Weak transcription	Stomach Mucosa	stomach
16	chr4:148906000-148925200	Weak transcription	Adipose Nuclei	Adipose
17	chr4:148906400-148928400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:148906600-148917600	Weak transcription	Gastric	stomach
19	chr4:148906600-148920600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:148906600-148920600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:148906600-148920800	Weak transcription	Fetal Intestine Small	intestine
22	chr4:148906800-148915000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:148906800-148918000	Weak transcription	NHLF	lung
24	chr4:148907000-148914600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:148907200-148928000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:148907400-148928400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:148907800-148920600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:148909000-148914600	Weak transcription	HSMM	muscle
29	chr4:148910200-148914600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:148910200-148914800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr4:148910200-148928400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:148911400-148914600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:148911600-148915400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:148911600-148936200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:148911800-148917600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:148911800-148925200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:148912200-148913800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr4:148912400-148916600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:148912600-148916600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr4:148912800-148914600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:148913000-148913800	Enhancers	Psoas Muscle	Psoas
42	chr4:148913000-148915400	Weak transcription	Ovary	ovary
43	chr4:148913000-148920000	Weak transcription	GM12878-XiMat	blood
44	chr4:148913200-148914600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:148913200-148916000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:148913200-148929200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:148913400-148914200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:148913400-148914400	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:148913400-148914600	Weak transcription	Fetal Kidney	kidney
50	chr4:148913400-148914600	Weak transcription	Left Ventricle	heart

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