Variant report

Variant	rs11978542
Chromosome Location	chr7:5015551-5015552
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:5015456-5015559	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:5015367-5015573	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:5013631..5016563-chr7:5022027..5023765,2	K562	blood:
2	chr7:5012983..5015694-chr7:5819277..5821133,2	K562	blood:

Variant related genes	Relation type
RNF216P1	TF binding region
ENSG00000011275	Chromatin interaction
ENSG00000196204	Chromatin interaction
ENSG00000272968	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11972112	0.84[EUR][1000 genomes]
rs55661736	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55707232	0.83[EUR][1000 genomes]
rs56678056	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57433326	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73045974	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73045983	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
4	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
5	nsv8033	chr7:4802287-5086597	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1022678	chr7:4810626-5113387	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv538705	chr7:4810626-5113387	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1021170	chr7:4831361-5058033	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv538706	chr7:4831361-5058033	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1025467	chr7:4850447-5021443	ZNF genes & repeats Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1033855	chr7:4862677-5069764	Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
13	nsv1019120	chr7:4929653-5138409	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv917078	chr7:4962123-5151633	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent/Poised TSS 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
15	nsv525289	chr7:5003373-5083741	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5013800-5015600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:5014400-5016600	Weak transcription	Spleen	Spleen
3	chr7:5014600-5015600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr7:5014600-5015600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:5014600-5015600	Enhancers	Adipose Nuclei	Adipose
6	chr7:5014600-5016000	Weak transcription	Fetal Kidney	kidney
7	chr7:5014600-5016200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:5014600-5016200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr7:5014600-5016200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:5014600-5016200	Weak transcription	HSMMtube	muscle
11	chr7:5014600-5016400	Weak transcription	Brain Substantia Nigra	brain
12	chr7:5014600-5016400	Weak transcription	Left Ventricle	heart
13	chr7:5014600-5016600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:5014600-5016600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:5014600-5016600	Weak transcription	Esophagus	oesophagus
16	chr7:5014600-5016600	Weak transcription	Lung	lung
17	chr7:5014600-5016800	Weak transcription	Gastric	stomach
18	chr7:5014600-5016800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:5014600-5017200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:5014600-5023800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:5014600-5024400	Weak transcription	Small Intestine	intestine
22	chr7:5014600-5036200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr7:5014600-5041000	Weak transcription	Stomach Mucosa	stomach
24	chr7:5014800-5015600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr7:5014800-5015600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr7:5014800-5015600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:5014800-5015600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr7:5014800-5015800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr7:5014800-5016000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr7:5014800-5016000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr7:5014800-5016200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr7:5014800-5016200	Weak transcription	Fetal Thymus	thymus
33	chr7:5014800-5016400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr7:5014800-5016400	Weak transcription	Placenta	Placenta
35	chr7:5014800-5016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr7:5014800-5016600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr7:5014800-5016600	Weak transcription	Aorta	Aorta
38	chr7:5014800-5016600	Weak transcription	Fetal Intestine Large	intestine
39	chr7:5014800-5016600	Weak transcription	Fetal Stomach	stomach
40	chr7:5014800-5016600	Weak transcription	Ovary	ovary
41	chr7:5014800-5016600	Weak transcription	Pancreas	Pancrea
42	chr7:5014800-5016600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:5014800-5016600	Weak transcription	Thymus	Thymus
44	chr7:5014800-5024400	Weak transcription	Colonic Mucosa	Colon
45	chr7:5014800-5026200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr7:5014800-5040000	Weak transcription	Right Atrium	heart
47	chr7:5014800-5041400	Weak transcription	Fetal Heart	heart
48	chr7:5015000-5015600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:5015000-5015600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr7:5015000-5015600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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