Variant report

Variant	rs7939039
Chromosome Location	chr11:100561690-100561691
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:100555471..100559429-chr11:100560336..100563382,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165895	Chromatin interaction
ENSG00000248027	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10160651	0.84[AFR][1000 genomes]
rs11224386	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11224394	1.00[AMR][1000 genomes]
rs12285737	1.00[AMR][1000 genomes]
rs12288213	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57756191	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7114498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7115557	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7126783	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73571424	0.90[AFR][1000 genomes]
rs73573318	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73573332	0.84[AFR][1000 genomes]
rs7927982	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7933066	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7942169	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053430	chr11:99888390-100629136	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1042067	chr11:99889697-100629136	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv556122	chr11:99893282-100585889	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1037689	chr11:99895378-100624599	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1040942	chr11:99895378-100629136	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1039852	chr11:99901695-100610533	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer 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	7 gene(s)	inside rSNPs	diseases
7	nsv541152	chr11:99901695-100610533	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1045190	chr11:99913193-100627395	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv541153	chr11:99913193-100627395	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv529454	chr11:99913394-100627255	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1043022	chr11:100387466-100610533	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv832246	chr11:100426725-100606957	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100559400-100562600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr11:100559400-100563200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:100559400-100564400	Weak transcription	Psoas Muscle	Psoas
4	chr11:100559800-100562600	Weak transcription	Hela-S3	cervix
5	chr11:100559800-100574600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:100559800-100580000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr11:100559800-100580000	Weak transcription	HSMM	muscle
8	chr11:100560000-100566800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:100560200-100562800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:100560200-100563200	Weak transcription	A549	lung
11	chr11:100560200-100573800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:100560200-100576400	Weak transcription	Primary B cells from cord blood	blood
13	chr11:100560200-100580000	Weak transcription	NH-A	brain
14	chr11:100560200-100580600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:100560400-100565200	Weak transcription	Fetal Intestine Small	intestine
16	chr11:100560400-100571000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:100560600-100564200	Weak transcription	Fetal Kidney	kidney
18	chr11:100560600-100571200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr11:100560800-100562200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:100560800-100563200	Weak transcription	Adipose Nuclei	Adipose
21	chr11:100560800-100563200	Weak transcription	Gastric	stomach
22	chr11:100560800-100563200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:100560800-100563200	Weak transcription	Stomach Mucosa	stomach
24	chr11:100560800-100563400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr11:100560800-100565200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:100560800-100565200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:100560800-100565600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr11:100560800-100565600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:100560800-100565800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr11:100560800-100566600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr11:100560800-100569000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:100560800-100571200	Weak transcription	Fetal Intestine Large	intestine
33	chr11:100560800-100571600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:100560800-100574400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr11:100560800-100574600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:100560800-100578400	Weak transcription	Pancreas	Pancrea
37	chr11:100560800-100580200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:100561000-100562400	Weak transcription	HMEC	breast
39	chr11:100561000-100562400	Weak transcription	NHEK	skin
40	chr11:100561000-100563000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr11:100561000-100563000	Weak transcription	HSMMtube	muscle
42	chr11:100561000-100563200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:100561000-100563200	Weak transcription	Liver	Liver
44	chr11:100561000-100563200	Weak transcription	Fetal Muscle Leg	muscle
45	chr11:100561000-100563200	Weak transcription	Spleen	Spleen
46	chr11:100561000-100564000	Weak transcription	Fetal Heart	heart
47	chr11:100561000-100564600	Weak transcription	Fetal Stomach	stomach
48	chr11:100561000-100564800	Weak transcription	Left Ventricle	heart
49	chr11:100561000-100566400	Weak transcription	Esophagus	oesophagus
50	chr11:100561000-100570600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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