Variant report

Variant	rs72965644
Chromosome Location	chr4:152041890-152041891
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	chr4:152019971..152022516-chr4:152039598..152042483,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3D19-2	chr4:152041843-152041963	NONHSAT098742

Variant related genes	Relation type
ENSG00000145425	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10452218	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2897661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58288902	0.81[AFR][1000 genomes]
rs72965652	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965662	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965663	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965675	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1018404	chr4:151664438-152067409	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1017850	chr4:151664438-152071876	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers 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 miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv2763837	chr4:151664438-152071888	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv870257	chr4:151665349-152072867	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1015387	chr4:151673751-152071876	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv526976	chr4:151675819-152055073	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv949066	chr4:151693149-152069566	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv949002	chr4:151693149-152095109	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1031720	chr4:151708502-152071876	Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
15	nsv1031516	chr4:151718614-152065644	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
16	nsv537304	chr4:151718614-152065644	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
17	nsv1022884	chr4:151718814-152065505	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
18	nsv537305	chr4:151718814-152065505	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
19	nsv595690	chr4:151788955-152109552	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
20	nsv1026416	chr4:151847403-152105879	Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
21	nsv1018797	chr4:151913585-152073419	Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
22	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
23	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
24	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152022800-152069800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:152025000-152073200	Weak transcription	Stomach Mucosa	stomach
3	chr4:152025200-152073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:152025200-152085400	Weak transcription	Hela-S3	cervix
5	chr4:152025600-152042600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:152026200-152042200	Weak transcription	NHDF-Ad	bronchial
7	chr4:152027000-152086600	Weak transcription	Fetal Kidney	kidney
8	chr4:152027200-152050400	Weak transcription	Aorta	Aorta
9	chr4:152027200-152095600	Weak transcription	Pancreas	Pancrea
10	chr4:152027800-152042600	Weak transcription	Colonic Mucosa	Colon
11	chr4:152027800-152047200	Weak transcription	HSMMtube	muscle
12	chr4:152027800-152050800	Weak transcription	Spleen	Spleen
13	chr4:152027800-152065000	Weak transcription	Gastric	stomach
14	chr4:152028000-152047200	Weak transcription	Esophagus	oesophagus
15	chr4:152028600-152043600	Weak transcription	Small Intestine	intestine
16	chr4:152028600-152048600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:152028600-152065600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:152028800-152049000	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:152029200-152046000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:152029200-152047200	Weak transcription	Brain Angular Gyrus	brain
21	chr4:152029200-152048400	Weak transcription	HMEC	breast
22	chr4:152029200-152060800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:152029200-152065200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:152029200-152070600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:152029400-152042600	Weak transcription	Placenta	Placenta
26	chr4:152029600-152042400	Weak transcription	Brain Anterior Caudate	brain
27	chr4:152031800-152048600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:152031800-152052800	Weak transcription	Fetal Brain Female	brain
29	chr4:152033000-152059000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:152033400-152045600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:152033600-152044600	Weak transcription	Lung	lung
32	chr4:152034200-152043200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:152034200-152048400	Weak transcription	A549	lung
34	chr4:152034400-152042000	Weak transcription	Brain Germinal Matrix	brain
35	chr4:152034400-152046000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:152034600-152042800	Weak transcription	NHEK	skin
37	chr4:152034800-152050600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:152035000-152048400	Weak transcription	Brain Substantia Nigra	brain
39	chr4:152035200-152042600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr4:152035200-152047000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:152035400-152042600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:152035600-152072400	Weak transcription	Fetal Brain Male	brain
43	chr4:152036000-152042000	Weak transcription	NH-A	brain
44	chr4:152036000-152046400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:152036000-152047200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:152036200-152042800	Weak transcription	NHLF	lung
47	chr4:152036200-152047200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:152036600-152058400	Weak transcription	Fetal Heart	heart
49	chr4:152036800-152049200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:152038800-152042600	Weak transcription	HepG2	liver

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