Variant report

Variant	rs780130
Chromosome Location	chr5:179957492-179957493
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	chr5:179920138..179923580-chr5:179954774..179958751,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113300	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12656468	1.00[ASN][1000 genomes]
rs2940546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729882	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
10	nsv1019519	chr5:179866730-179959408	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv1810959	chr5:179945112-179997861	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179929000-179959200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:179933800-179959000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:179942000-179958800	Weak transcription	Esophagus	oesophagus
4	chr5:179942600-179959000	Weak transcription	HepG2	liver
5	chr5:179946000-179958400	Weak transcription	Lung	lung
6	chr5:179946200-179960800	Weak transcription	NHLF	lung
7	chr5:179946800-179959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:179947000-179958000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:179949800-179958800	Weak transcription	Aorta	Aorta
10	chr5:179950200-179958600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:179950200-179959000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:179950200-179959200	Weak transcription	Brain Anterior Caudate	brain
13	chr5:179950200-179959200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:179950200-179959800	Weak transcription	Left Ventricle	heart
15	chr5:179950200-179975200	Weak transcription	Psoas Muscle	Psoas
16	chr5:179950200-179984400	Weak transcription	NHDF-Ad	bronchial
17	chr5:179950200-179992000	Weak transcription	Right Ventricle	heart
18	chr5:179950400-179992400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:179950600-179959400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:179950600-180004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:179950800-179959000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:179951000-179959200	Weak transcription	Fetal Brain Male	brain
23	chr5:179951000-179959400	Weak transcription	NHEK	skin
24	chr5:179951000-179991800	Weak transcription	Small Intestine	intestine
25	chr5:179951200-179959200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:179951400-179959200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr5:179951600-179959000	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:179951600-179967000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:179952400-179969000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:179952800-179958800	Weak transcription	Thymus	Thymus
31	chr5:179952800-179959200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr5:179952800-179967200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr5:179952800-179975400	Weak transcription	Stomach Mucosa	stomach
34	chr5:179953000-179959600	Weak transcription	Placenta	Placenta
35	chr5:179953200-179958600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:179953200-179959200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:179953400-179975200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:179953600-179958200	Weak transcription	Spleen	Spleen
39	chr5:179953600-179959200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr5:179953600-179959200	Weak transcription	Brain Angular Gyrus	brain
41	chr5:179953600-179977000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr5:179953800-179975400	Weak transcription	Fetal Heart	heart
43	chr5:179954000-179962600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:179954000-179964400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:179954200-179957600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr5:179954400-179957600	Strong transcription	Fetal Thymus	thymus
47	chr5:179954400-179959000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:179954600-179957600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:179954600-179957600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:179954600-179957600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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