Variant report

Variant	rs4560546
Chromosome Location	chr5:16781440-16781441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10074151	0.84[AMR][1000 genomes]
rs11133858	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2052836	0.81[AMR][1000 genomes]
rs2052837	0.81[AMR][1000 genomes]
rs2052838	0.84[AMR][1000 genomes]
rs6877202	0.82[AMR][1000 genomes]
rs6878154	0.84[AMR][1000 genomes]
rs6888845	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs747056	0.82[AMR][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	nsv880373	chr5:16710572-16785604	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16741200-16782000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:16748600-16783800	Weak transcription	Small Intestine	intestine
3	chr5:16755200-16795400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:16757600-16796800	Weak transcription	Right Ventricle	heart
5	chr5:16759800-16783600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:16760000-16791400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:16761000-16796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:16762400-16784000	Weak transcription	Colonic Mucosa	Colon
9	chr5:16763200-16782200	Weak transcription	Fetal Brain Male	brain
10	chr5:16763800-16794600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:16764200-16784000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:16764600-16783800	Weak transcription	Spleen	Spleen
13	chr5:16764600-16792800	Weak transcription	Stomach Mucosa	stomach
14	chr5:16764600-16807400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:16766800-16785200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:16767200-16781800	Weak transcription	Ovary	ovary
17	chr5:16768600-16781800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:16769200-16781800	Weak transcription	Lung	lung
19	chr5:16770200-16791400	Weak transcription	Fetal Kidney	kidney
20	chr5:16770800-16792400	Weak transcription	Placenta	Placenta
21	chr5:16770800-16793800	Weak transcription	Hela-S3	cervix
22	chr5:16771000-16781600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:16773200-16781800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:16775200-16784400	Weak transcription	Psoas Muscle	Psoas
25	chr5:16775200-16796800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:16776200-16785400	Strong transcription	HUVEC	blood vessel
27	chr5:16776800-16782200	Strong transcription	HSMM	muscle
28	chr5:16776800-16784800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr5:16777000-16783400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:16777000-16783800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:16777200-16782800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:16777200-16785600	Strong transcription	Fetal Intestine Small	intestine
33	chr5:16777400-16784000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:16777600-16783200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:16777600-16783200	Strong transcription	HSMMtube	muscle
36	chr5:16777600-16784000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:16777800-16785200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr5:16777800-16786200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:16778200-16783200	Strong transcription	Fetal Muscle Leg	muscle
40	chr5:16778200-16784600	Strong transcription	Fetal Intestine Large	intestine
41	chr5:16778400-16782800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr5:16778600-16781800	Weak transcription	NHLF	lung
43	chr5:16778600-16784000	Strong transcription	A549	lung
44	chr5:16778800-16781800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr5:16778800-16783000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:16778800-16783400	Strong transcription	NH-A	brain
47	chr5:16778800-16784600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:16778800-16800000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:16779200-16781800	Weak transcription	NHEK	skin
50	chr5:16779200-16783400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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