Variant report

Variant	rs72953389
Chromosome Location	chr6:74423994-74423995
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	chr6:74405796..74408652-chr6:74422583..74424647,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156535	Chromatin interaction
ENSG00000231652	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs45620342	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72953390	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72953401	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9442950	0.93[AFR][1000 genomes]
rs9446990	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9446991	0.93[AFR][1000 genomes]
rs9446992	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9446993	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
2	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
3	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
5	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
6	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv463154	chr6:74412048-74775904	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv603695	chr6:74412048-74775904	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72953389	ENSG00000156535	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74407200-74424800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:74407600-74424000	Weak transcription	Right Ventricle	heart
3	chr6:74408000-74446800	Weak transcription	Dnd41	blood
4	chr6:74414400-74424000	Weak transcription	Placenta	Placenta
5	chr6:74414800-74474600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:74415200-74432200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:74417000-74424000	Weak transcription	Esophagus	oesophagus
8	chr6:74420400-74425200	Enhancers	Primary hematopoietic stem cells	blood
9	chr6:74421000-74424600	Weak transcription	Hela-S3	cervix
10	chr6:74421000-74432200	Weak transcription	HSMM	muscle
11	chr6:74422000-74424200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:74422200-74424400	Enhancers	Adipose Nuclei	Adipose
13	chr6:74422200-74424600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:74422200-74425000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:74422400-74424400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr6:74422400-74424400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:74422600-74424200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr6:74422600-74424200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr6:74422600-74425400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:74422600-74432000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:74422800-74424000	Weak transcription	Fetal Lung	lung
22	chr6:74422800-74424000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:74423000-74424200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr6:74423000-74424200	Enhancers	Primary T cells from cord blood	blood
25	chr6:74423000-74424200	Enhancers	Fetal Thymus	thymus
26	chr6:74423000-74424200	Enhancers	Left Ventricle	heart
27	chr6:74423000-74424200	Enhancers	Right Atrium	heart
28	chr6:74423000-74424400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:74423000-74424400	Enhancers	Brain Substantia Nigra	brain
30	chr6:74423000-74424800	Genic enhancers	NHDF-Ad	bronchial
31	chr6:74423000-74425000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:74423000-74425200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:74423200-74424000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:74423200-74424200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr6:74423200-74424200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:74423200-74424200	Enhancers	Colon Smooth Muscle	Colon
37	chr6:74423200-74424400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr6:74423200-74424400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr6:74423200-74424400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr6:74423200-74424400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr6:74423200-74424400	Enhancers	Lung	lung
42	chr6:74423200-74424400	Flanking Active TSS	HUVEC	blood vessel
43	chr6:74423200-74424800	Enhancers	NH-A	brain
44	chr6:74423200-74425200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:74423200-74425400	Enhancers	Osteobl	bone
46	chr6:74423400-74424200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr6:74423400-74424200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:74423400-74424400	Enhancers	Primary B cells from peripheral blood	blood
49	chr6:74423400-74424400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:74423400-74424600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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