Variant report

Variant	rs2052838
Chromosome Location	chr5:16787141-16787142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16744168..16745132-chr5:16787048..16788082,8	MCF-7	breast:
2	chr5:16784701..16787932-chr5:16789785..16793090,3	MCF-7	breast:
3	chr5:16786713..16788907-chr5:16934226..16936719,3	MCF-7	breast:
4	chr5:16744168..16745132-chr5:16787048..16788082,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10074151	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780098	0.83[AMR][1000 genomes]
rs11133858	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2052836	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2052837	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs25902	0.83[EUR][1000 genomes]
rs25906	0.81[EUR][1000 genomes]
rs31570	0.84[EUR][1000 genomes]
rs31572	0.84[EUR][1000 genomes]
rs4560546	0.84[AMR][1000 genomes]
rs6877202	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6877321	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6877325	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6877702	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6878154	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6888845	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs747056	0.95[AMR][1000 genomes];0.92[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	nsv964758	chr5:16783252-16787402	Weak transcription Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 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	chr5:16760000-16791400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:16761000-16796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:16763800-16794600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:16764600-16792800	Weak transcription	Stomach Mucosa	stomach
7	chr5:16764600-16807400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:16770200-16791400	Weak transcription	Fetal Kidney	kidney
9	chr5:16770800-16792400	Weak transcription	Placenta	Placenta
10	chr5:16770800-16793800	Weak transcription	Hela-S3	cervix
11	chr5:16775200-16796800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:16778800-16800000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:16779400-16791400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:16779800-16796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:16779800-16797200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:16780200-16791000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:16780800-16791400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:16783000-16788200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:16783000-16797000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:16783000-16797400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:16783200-16791400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:16783400-16792600	Weak transcription	Lung	lung
23	chr5:16783400-16796800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:16783400-16810000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:16784400-16788200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:16784400-16796800	Weak transcription	HMEC	breast
27	chr5:16784600-16788200	Weak transcription	Fetal Intestine Large	intestine
28	chr5:16784600-16789400	Weak transcription	HepG2	liver
29	chr5:16784600-16809200	Weak transcription	Ovary	ovary
30	chr5:16784800-16788800	Weak transcription	NHLF	lung
31	chr5:16784800-16789000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:16784800-16794600	Weak transcription	Gastric	stomach
33	chr5:16785000-16788200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr5:16785000-16791400	Weak transcription	Psoas Muscle	Psoas
35	chr5:16785200-16788200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:16785200-16791400	Weak transcription	Fetal Lung	lung
37	chr5:16785200-16792400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:16785200-16794600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:16785400-16787800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:16785400-16788200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:16785400-16788200	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:16785400-16788400	Weak transcription	HUVEC	blood vessel
43	chr5:16785400-16788400	Weak transcription	NHEK	skin
44	chr5:16785400-16791400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:16785400-16791400	Weak transcription	HSMMtube	muscle
46	chr5:16785400-16792000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr5:16785400-16792400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:16785400-16794600	Weak transcription	Spleen	Spleen
49	chr5:16785400-16796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:16785600-16788200	Weak transcription	Fetal Intestine Small	intestine

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