Variant report

Variant	rs253359
Chromosome Location	chr5:16793034-16793035
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	chr5:16784701..16787932-chr5:16789785..16793090,3	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10037139	0.83[EUR][1000 genomes]
rs153409	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs185236	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs250349	0.86[EUR][1000 genomes]
rs250353	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs250356	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs253363	0.83[EUR][1000 genomes]
rs253365	0.89[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs253366	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs253367	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs253370	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28297	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs33401	0.85[CEU][hapmap]
rs385552	0.83[EUR][1000 genomes]
rs40020	0.85[CEU][hapmap]
rs451009	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs496033	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6888120	0.85[CEU][hapmap];0.84[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	esv3529928	chr5:16748426-16856563	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3529929	chr5:16748426-16856563	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv1030550	chr5:16748966-16872084	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	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
6	nsv597309	chr5:16791857-16837862	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16755200-16795400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:16757600-16796800	Weak transcription	Right Ventricle	heart
3	chr5:16761000-16796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:16763800-16794600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:16764600-16807400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:16770800-16793800	Weak transcription	Hela-S3	cervix
7	chr5:16775200-16796800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:16778800-16800000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:16779800-16796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:16779800-16797200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:16783000-16797000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:16783000-16797400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:16783400-16796800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:16783400-16810000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:16784400-16796800	Weak transcription	HMEC	breast
16	chr5:16784600-16809200	Weak transcription	Ovary	ovary
17	chr5:16784800-16794600	Weak transcription	Gastric	stomach
18	chr5:16785200-16794600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:16785400-16794600	Weak transcription	Spleen	Spleen
20	chr5:16785400-16796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:16785800-16804200	Weak transcription	HSMM	muscle
22	chr5:16788600-16799800	Weak transcription	Pancreas	Pancrea
23	chr5:16789200-16797200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:16789400-16809200	Weak transcription	NHLF	lung
25	chr5:16790600-16796600	Weak transcription	HUVEC	blood vessel
26	chr5:16790800-16797000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr5:16791200-16796400	Enhancers	Fetal Brain Male	brain
28	chr5:16791400-16793200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:16791600-16793200	Enhancers	Brain Germinal Matrix	brain
30	chr5:16791600-16793200	Enhancers	Fetal Brain Female	brain
31	chr5:16791800-16793200	Genic enhancers	A549	lung
32	chr5:16791800-16795000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:16791800-16796600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:16791800-16796800	Weak transcription	NHEK	skin
35	chr5:16791800-16800600	Weak transcription	Osteobl	bone
36	chr5:16791800-16807000	Weak transcription	Fetal Kidney	kidney
37	chr5:16791800-16807400	Weak transcription	Psoas Muscle	Psoas
38	chr5:16792000-16796600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:16792000-16796600	Weak transcription	NH-A	brain
40	chr5:16792200-16793800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:16792400-16793200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:16792400-16793200	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr5:16792400-16793400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr5:16792400-16795400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:16792400-16795400	Strong transcription	Fetal Intestine Small	intestine
46	chr5:16792600-16793400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr5:16792600-16795200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:16792600-16795200	Strong transcription	Fetal Intestine Large	intestine
49	chr5:16792600-16798800	Weak transcription	Esophagus	oesophagus
50	chr5:16792800-16793200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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