Variant report

Variant	rs13178371
Chromosome Location	chr5:16920944-16920945
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	chr5:16920267..16924457-chr5:16934356..16936911,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13154383	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13154695	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13155144	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13171937	0.84[AMR][1000 genomes]
rs13172299	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13172386	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13172506	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13172712	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13178606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13178744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17542583	0.90[AMR][1000 genomes]
rs17614456	0.90[AMR][1000 genomes]
rs17614462	0.90[AMR][1000 genomes]
rs34162327	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34214603	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34222409	0.90[AMR][1000 genomes]
rs34689597	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34738746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34989400	0.90[AMR][1000 genomes]
rs35151606	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609335	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609336	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609337	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609338	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609339	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609340	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609341	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609344	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active 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 miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16902200-16930000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:16904400-16933200	Weak transcription	Fetal Stomach	stomach
3	chr5:16910800-16924000	Weak transcription	Small Intestine	intestine
4	chr5:16913800-16922600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:16914000-16931600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:16914000-16933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:16914200-16930200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:16914600-16934400	Weak transcription	Psoas Muscle	Psoas
9	chr5:16915000-16924000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:16915200-16921800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr5:16915400-16924000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:16916000-16930800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:16916800-16922600	Weak transcription	Fetal Intestine Small	intestine
14	chr5:16917000-16924000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:16918400-16922600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:16918400-16930400	Weak transcription	HSMMtube	muscle
17	chr5:16918600-16921400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:16918600-16930400	Weak transcription	HSMM	muscle
19	chr5:16918600-16930600	Weak transcription	NH-A	brain
20	chr5:16918800-16924400	Enhancers	Pancreas	Pancrea
21	chr5:16919200-16924000	Weak transcription	Fetal Lung	lung
22	chr5:16919200-16930000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:16919200-16931600	Weak transcription	HMEC	breast
24	chr5:16919600-16921200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:16919600-16921400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:16919600-16921400	Weak transcription	Ovary	ovary
27	chr5:16919600-16921400	Weak transcription	HUVEC	blood vessel
28	chr5:16919600-16921400	Weak transcription	NHLF	lung
29	chr5:16919600-16921800	Weak transcription	Gastric	stomach
30	chr5:16919600-16923200	Weak transcription	Fetal Intestine Large	intestine
31	chr5:16919600-16924000	Weak transcription	Placenta	Placenta
32	chr5:16919600-16929600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:16919800-16921400	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:16919800-16921400	Weak transcription	Osteobl	bone
35	chr5:16920200-16921800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:16920200-16926200	Enhancers	Stomach Mucosa	stomach
37	chr5:16920400-16921400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:16920400-16921600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:16920400-16922000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr5:16920400-16922600	Weak transcription	Lung	lung
41	chr5:16920600-16921000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:16920600-16921000	Genic enhancers	NHEK	skin
43	chr5:16920800-16921400	Enhancers	A549	lung
44	chr5:16920800-16921400	Weak transcription	NHDF-Ad	bronchial
45	chr5:16920800-16921800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:16920800-16924400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr5:16920800-16930800	Weak transcription	Fetal Kidney	kidney

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