Variant report

Variant	rs250354
Chromosome Location	chr5:16792135-16792136
allele	G/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:
2	chr5:16791046..16792329-chr5:17190230..17191251,5	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs152705	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs152706	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs171628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs173787	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs250346	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs250347	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs250348	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs250350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs250355	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs253361	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33400	0.83[ASN][1000 genomes]
rs396514	0.88[EUR][1000 genomes];0.93[ASN][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:66 , 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	chr5:16764600-16792800	Weak transcription	Stomach Mucosa	stomach
6	chr5:16764600-16807400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:16770800-16792400	Weak transcription	Placenta	Placenta
8	chr5:16770800-16793800	Weak transcription	Hela-S3	cervix
9	chr5:16775200-16796800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:16778800-16800000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:16779800-16796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:16779800-16797200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:16783000-16797000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:16783000-16797400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:16783400-16792600	Weak transcription	Lung	lung
16	chr5:16783400-16796800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:16783400-16810000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:16784400-16796800	Weak transcription	HMEC	breast
19	chr5:16784600-16809200	Weak transcription	Ovary	ovary
20	chr5:16784800-16794600	Weak transcription	Gastric	stomach
21	chr5:16785200-16792400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:16785200-16794600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:16785400-16792400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:16785400-16794600	Weak transcription	Spleen	Spleen
25	chr5:16785400-16796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:16785800-16792200	Weak transcription	Fetal Stomach	stomach
27	chr5:16785800-16804200	Weak transcription	HSMM	muscle
28	chr5:16788000-16792600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:16788600-16792400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:16788600-16799800	Weak transcription	Pancreas	Pancrea
31	chr5:16789000-16792400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:16789200-16792400	Weak transcription	Fetal Intestine Small	intestine
33	chr5:16789200-16792600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:16789200-16792600	Weak transcription	Fetal Intestine Large	intestine
35	chr5:16789200-16797200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:16789400-16809200	Weak transcription	NHLF	lung
37	chr5:16790200-16792400	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:16790600-16792400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:16790600-16796600	Weak transcription	HUVEC	blood vessel
40	chr5:16790800-16792400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:16790800-16792600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:16790800-16797000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr5:16791000-16792400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:16791200-16792800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:16791200-16792800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:16791200-16796400	Enhancers	Fetal Brain Male	brain
47	chr5:16791400-16792200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:16791400-16792400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr5:16791400-16792600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:16791400-16793000	Enhancers	Fetal Lung	lung

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