Variant report

Variant	rs4540325
Chromosome Location	chr7:4751840-4751841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:4680155..4683221-chr7:4751586..4755300,3	MCF-7	breast:
2	chr7:4746229..4748965-chr7:4749361..4752202,3	MCF-7	breast:
3	chr7:4750973..4755247-chr7:4763506..4767347,8	MCF-7	breast:
4	chr7:4746310..4749219-chr7:4749673..4751937,2	K562	blood:
5	chr7:4721886..4725324-chr7:4750034..4753367,6	MCF-7	breast:
6	chr7:4735653..4738746-chr7:4749677..4753916,3	K562	blood:
7	chr7:4725925..4727781-chr7:4750063..4752519,2	MCF-7	breast:
8	chr7:4747719..4749833-chr7:4750437..4753024,2	K562	blood:

Variant related genes	Relation type
ENSG00000164916	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10261971	0.86[JPT][hapmap]
rs3087749	0.86[JPT][hapmap]
rs4132809	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4523152	0.83[CEU][hapmap];0.89[CHB][hapmap];0.84[GIH][hapmap]
rs4724033	1.00[JPT][hapmap]
rs62453200	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6463011	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6944865	0.86[JPT][hapmap]
rs6968957	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6973046	0.86[JPT][hapmap]
rs7455271	0.96[CEU][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7781456	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv508442	chr7:4623264-4769628	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1019692	chr7:4724310-4756406	Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv887377	chr7:4730535-4862259	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv887378	chr7:4730535-4929721	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
9	nsv887379	chr7:4749527-4828593	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4725800-4754000	Weak transcription	HMEC	breast
2	chr7:4730200-4755800	Weak transcription	Thymus	Thymus
3	chr7:4730800-4761600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:4740600-4757400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr7:4743400-4752000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:4743400-4754800	Weak transcription	Aorta	Aorta
7	chr7:4743800-4763600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:4746000-4754400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr7:4746200-4752000	Weak transcription	HSMMtube	muscle
10	chr7:4746600-4752000	Weak transcription	Colonic Mucosa	Colon
11	chr7:4746600-4752400	Weak transcription	Primary B cells from cord blood	blood
12	chr7:4746600-4753200	Enhancers	Right Ventricle	heart
13	chr7:4746800-4752000	Weak transcription	NHDF-Ad	bronchial
14	chr7:4747000-4752200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:4747000-4754400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:4747400-4764600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:4747800-4752000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:4747800-4753800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:4747800-4754000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr7:4748000-4752600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:4748000-4757600	Weak transcription	Fetal Brain Male	brain
22	chr7:4748200-4752200	Weak transcription	Brain Anterior Caudate	brain
23	chr7:4748200-4752200	Weak transcription	Brain Hippocampus Middle	brain
24	chr7:4748400-4754400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:4748800-4756400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr7:4749000-4752000	Weak transcription	Fetal Heart	heart
27	chr7:4749000-4752400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:4749000-4754600	Weak transcription	Brain Germinal Matrix	brain
29	chr7:4749000-4763600	Weak transcription	HUVEC	blood vessel
30	chr7:4749200-4752600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:4749400-4752400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:4749400-4754400	Weak transcription	Brain Angular Gyrus	brain
33	chr7:4749400-4755800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:4749600-4754000	Weak transcription	Brain Substantia Nigra	brain
35	chr7:4749600-4754200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr7:4749800-4757200	Weak transcription	Hela-S3	cervix
37	chr7:4750000-4752800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr7:4750400-4752000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:4750400-4752400	Strong transcription	Fetal Thymus	thymus
40	chr7:4750400-4752600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:4750600-4752000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr7:4750600-4752000	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr7:4750600-4752200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:4750600-4752200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr7:4750600-4752200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr7:4750600-4753000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:4750600-4753600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:4750800-4752000	Enhancers	HepG2	liver
49	chr7:4750800-4752800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:4750800-4752800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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