Variant report

Variant	rs6789675
Chromosome Location	chr3:61554862-61554863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:61546210..61550751-chr3:61552901..61555613,6	MCF-7	breast:
2	chr3:61553485..61555425-chr3:61565373..61566963,2	MCF-7	breast:
3	chr3:61554363..61558137-chr3:61559653..61562085,4	MCF-7	breast:
4	chr3:61543024..61544973-chr3:61553525..61555086,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144724	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11713144	0.82[AMR][1000 genomes]
rs2886518	0.89[ASN][1000 genomes]
rs2886520	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35668148	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55822630	0.80[EUR][1000 genomes]
rs62268713	0.83[AMR][1000 genomes]
rs7621604	0.82[ASN][1000 genomes]
rs7638985	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv822105	chr3:61531517-61556259	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61550600-61568600	Weak transcription	Pancreas	Pancrea
2	chr3:61550800-61555400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:61550800-61556800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:61550800-61556800	Weak transcription	Ovary	ovary
5	chr3:61550800-61557600	Weak transcription	Psoas Muscle	Psoas
6	chr3:61550800-61558400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:61550800-61574200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:61551000-61555800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:61551000-61556800	Weak transcription	NH-A	brain
10	chr3:61551000-61557400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:61551000-61557600	Weak transcription	Aorta	Aorta
12	chr3:61551000-61557600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:61551000-61557600	Weak transcription	Right Atrium	heart
14	chr3:61551000-61559800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:61551000-61559800	Weak transcription	NHEK	skin
16	chr3:61551000-61561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:61551200-61555600	Weak transcription	Fetal Lung	lung
18	chr3:61551200-61555800	Weak transcription	Brain Anterior Caudate	brain
19	chr3:61551200-61556400	Weak transcription	Fetal Brain Male	brain
20	chr3:61551200-61557600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:61551200-61560000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:61551400-61555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:61551400-61555800	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:61551600-61555400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:61551600-61556800	Weak transcription	Right Ventricle	heart
26	chr3:61551600-61557600	Weak transcription	Fetal Kidney	kidney
27	chr3:61551600-61559800	Weak transcription	NHLF	lung
28	chr3:61551600-61563800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:61551800-61555200	Weak transcription	Brain Angular Gyrus	brain
30	chr3:61551800-61555600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:61551800-61556200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:61552000-61555600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:61552000-61555800	Weak transcription	Osteobl	bone
34	chr3:61552000-61556200	Weak transcription	HSMM	muscle
35	chr3:61552200-61555400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:61552200-61555400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:61552200-61555800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:61552200-61556800	Weak transcription	NHDF-Ad	bronchial
39	chr3:61552200-61563400	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:61552600-61555400	Weak transcription	Adipose Nuclei	Adipose
41	chr3:61552600-61556800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:61552600-61557200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:61552600-61557400	Weak transcription	Left Ventricle	heart
44	chr3:61552800-61557200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:61552800-61557400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr3:61553000-61555000	Weak transcription	Liver	Liver
47	chr3:61553000-61555400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:61553000-61558200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:61553200-61555400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:61553400-61559800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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