Variant report

Variant	rs71609339
Chromosome Location	chr5:16918304-16918305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16913685..16915580-chr5:16917350..16919929,2	MCF-7	breast:
2	chr5:16917379..16919664-chr5:16935730..16937418,2	MCF-7	breast:
3	chr5:16916910..16918830-chr5:16931583..16933515,2	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	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	0.95[AMR][1000 genomes]
rs13172386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13172506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13172712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13178371	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13178606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13178744	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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34214603	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34222409	0.90[AMR][1000 genomes]
rs34689597	0.85[EUR][1000 genomes]
rs34738746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34989400	0.90[AMR][1000 genomes]
rs35151606	0.82[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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609337	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609338	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609341	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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16902200-16919000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:16902200-16930000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:16904400-16933200	Weak transcription	Fetal Stomach	stomach
4	chr5:16910800-16924000	Weak transcription	Small Intestine	intestine
5	chr5:16912200-16919800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:16913800-16918800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:16913800-16922600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:16914000-16918800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:16914000-16931600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:16914000-16933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:16914200-16930200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:16914400-16918400	Enhancers	HSMMtube	muscle
13	chr5:16914400-16918800	Weak transcription	Lung	lung
14	chr5:16914600-16918600	Enhancers	HMEC	breast
15	chr5:16914600-16918800	Weak transcription	Pancreas	Pancrea
16	chr5:16914600-16934400	Weak transcription	Psoas Muscle	Psoas
17	chr5:16914800-16918800	Weak transcription	Fetal Intestine Large	intestine
18	chr5:16915000-16924000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:16915200-16919400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:16915200-16920800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:16915200-16921800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:16915400-16919400	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:16915400-16924000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:16915600-16919200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:16915600-16919200	Enhancers	NHDF-Ad	bronchial
26	chr5:16915600-16919600	Weak transcription	Stomach Mucosa	stomach
27	chr5:16916000-16918600	Enhancers	HSMM	muscle
28	chr5:16916000-16919200	Enhancers	Osteobl	bone
29	chr5:16916000-16919600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:16916000-16930800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:16916200-16918400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:16916200-16918800	Weak transcription	Gastric	stomach
33	chr5:16916400-16918800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:16916400-16918800	Weak transcription	Esophagus	oesophagus
35	chr5:16916400-16920000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:16916800-16922600	Weak transcription	Fetal Intestine Small	intestine
37	chr5:16917000-16924000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:16917200-16918600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr5:16917200-16918600	Enhancers	NH-A	brain
40	chr5:16917200-16919400	Enhancers	NHEK	skin
41	chr5:16917400-16918400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:16917400-16918800	Enhancers	HUVEC	blood vessel
43	chr5:16917400-16919600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:16917400-16919600	Enhancers	Ovary	ovary
45	chr5:16917600-16918600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:16917600-16919200	Enhancers	Hela-S3	cervix
47	chr5:16917600-16920200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:16917800-16918400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:16918000-16919000	Weak transcription	NHLF	lung
50	chr5:16918000-16919200	Enhancers	Fetal Lung	lung

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