Variant report

Variant	rs39896
Chromosome Location	chr5:16914516-16914517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16913129..16917002-chr5:16934060..16938960,5	MCF-7	breast:
2	chr5:16911519..16914596-chr5:16934738..16936991,3	MCF-7	breast:
3	chr5:16913685..16915580-chr5:16917350..16919929,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs253384	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs253385	0.97[ASN][1000 genomes]
rs29454	0.86[LWK][hapmap];0.83[AFR][1000 genomes]
rs31454	0.84[MEX][hapmap]

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:63 , 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	chr5:16909400-16914600	Enhancers	Pancreas	Pancrea
5	chr5:16909400-16916400	Enhancers	Ovary	ovary
6	chr5:16909800-16915600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:16910800-16924000	Weak transcription	Small Intestine	intestine
8	chr5:16911600-16914600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:16911600-16916400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:16912200-16914800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:16912200-16919800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:16912400-16914600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:16912400-16914600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:16912400-16914600	Enhancers	Esophagus	oesophagus
15	chr5:16912400-16915400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:16912600-16914600	Enhancers	NH-A	brain
17	chr5:16912600-16915600	Enhancers	Stomach Mucosa	stomach
18	chr5:16912800-16914600	Flanking Active TSS	HMEC	breast
19	chr5:16912800-16914800	Enhancers	Fetal Intestine Large	intestine
20	chr5:16912800-16915200	Enhancers	HUVEC	blood vessel
21	chr5:16912800-16915600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr5:16913000-16915400	Enhancers	Fetal Muscle Leg	muscle
23	chr5:16913000-16916200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:16913400-16914600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr5:16913400-16914600	Enhancers	Colonic Mucosa	Colon
26	chr5:16913400-16914800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:16913400-16915400	Transcr. at gene 5' and 3'	A549	lung
28	chr5:16913600-16914600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:16913600-16914600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:16913600-16914600	Enhancers	Psoas Muscle	Psoas
31	chr5:16913600-16914600	Enhancers	Spleen	Spleen
32	chr5:16913600-16914600	Flanking Active TSS	HSMM	muscle
33	chr5:16913600-16915000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr5:16913600-16915000	Enhancers	Fetal Muscle Trunk	muscle
35	chr5:16913800-16914600	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr5:16913800-16914600	Enhancers	Placenta	Placenta
37	chr5:16913800-16914800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:16913800-16915400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:16913800-16916800	Weak transcription	Fetal Brain Male	brain
40	chr5:16913800-16918800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:16913800-16922600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:16914000-16914600	Genic enhancers	NHLF	lung
43	chr5:16914000-16916200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:16914000-16918800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr5:16914000-16931600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:16914000-16933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:16914200-16914600	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr5:16914200-16914600	Transcr. at gene 5' and 3'	NHEK	skin
49	chr5:16914200-16914800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr5:16914200-16915000	Active TSS	Duodenum Mucosa	Duodenum

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