Variant report

Variant	rs71609335
Chromosome Location	chr5:16916118-16916119
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	chr5:16913129..16917002-chr5:16934060..16938960,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs13154383	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13154695	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13155144	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13172299	0.89[AMR][1000 genomes]
rs13172386	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13172506	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13172712	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13178371	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13178606	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13178744	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17542583	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs17614456	0.95[AMR][1000 genomes]
rs17614462	0.95[AMR][1000 genomes]
rs34162327	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34214603	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34222409	0.95[AMR][1000 genomes]
rs34689597	0.85[EUR][1000 genomes]
rs34738746	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34989400	0.95[AMR][1000 genomes]
rs35151606	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609336	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609337	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609338	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609339	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609340	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609341	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609342	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71609344	0.89[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:56 , 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	chr5:16909400-16916400	Enhancers	Ovary	ovary
5	chr5:16910800-16924000	Weak transcription	Small Intestine	intestine
6	chr5:16911600-16916400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:16912200-16919800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:16913000-16916200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:16913800-16916800	Weak transcription	Fetal Brain Male	brain
10	chr5:16913800-16918800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:16913800-16922600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:16914000-16916200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:16914000-16918800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:16914000-16931600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:16914000-16933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:16914200-16916200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:16914200-16918000	Weak transcription	Fetal Lung	lung
18	chr5:16914200-16930200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:16914400-16916200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:16914400-16918400	Enhancers	HSMMtube	muscle
21	chr5:16914400-16918800	Weak transcription	Lung	lung
22	chr5:16914600-16916400	Genic enhancers	NHEK	skin
23	chr5:16914600-16917400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:16914600-16917400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:16914600-16918600	Enhancers	HMEC	breast
26	chr5:16914600-16918800	Weak transcription	Pancreas	Pancrea
27	chr5:16914600-16934400	Weak transcription	Psoas Muscle	Psoas
28	chr5:16914800-16917600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:16914800-16917600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:16914800-16918800	Weak transcription	Fetal Intestine Large	intestine
31	chr5:16915000-16924000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:16915200-16916200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:16915200-16919400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:16915200-16920800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr5:16915200-16921800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr5:16915400-16916200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:16915400-16916200	Enhancers	Gastric	stomach
38	chr5:16915400-16916200	Enhancers	Hela-S3	cervix
39	chr5:16915400-16919400	Weak transcription	Fetal Muscle Leg	muscle
40	chr5:16915400-16924000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:16915600-16916400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr5:16915600-16916400	Enhancers	Esophagus	oesophagus
43	chr5:16915600-16919200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:16915600-16919200	Enhancers	NHDF-Ad	bronchial
45	chr5:16915600-16919600	Weak transcription	Stomach Mucosa	stomach
46	chr5:16915800-16916400	Enhancers	HUVEC	blood vessel
47	chr5:16915800-16916800	Enhancers	Fetal Intestine Small	intestine
48	chr5:16916000-16916200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr5:16916000-16916400	Transcr. at gene 5' and 3'	A549	lung
50	chr5:16916000-16916400	Genic enhancers	NHLF	lung

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