Variant report

Variant	rs4888368
Chromosome Location	chr16:75305331-75305332
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75298255..75301654-chr16:75302973..75305723,3	K562	blood:
2	chr14:32394037..32396201-chr16:75304956..75307730,2	MCF-7	breast:
3	chr16:75304486..75306139-chr16:75308404..75310114,2	K562	blood:

Variant related genes	Relation type
ENSG00000050820	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1001861	0.86[ASN][1000 genomes]
rs12919951	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12928974	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2865826	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2865827	0.84[ASN][1000 genomes]
rs4594277	0.80[ASN][1000 genomes]
rs999674	0.84[ASN][1000 genomes]
rs999675	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv516504	chr16:75223491-75306402	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	esv1806781	chr16:75235390-75307470	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv906909	chr16:75236154-75316074	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	esv1792587	chr16:75237936-75305783	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv906910	chr16:75251299-75316074	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv906912	chr16:75252526-75320827	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
13	nsv906913	chr16:75267743-75306402	Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
14	nsv471095	chr16:75269533-75320827	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
15	nsv833283	chr16:75302175-75392308	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4888368	RP11-252K23.2	cis	Thyroid	GTEx
rs4888368	RP11-252K23.2	cis	Artery Tibial	GTEx
rs4888368	CFDP1	Cis_1M	lymphoblastoid	RTeQTL
rs4888368	BCAR1	cis	Esophagus Mucosa	GTEx
rs4888368	RP11-252K23.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75300600-75305600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:75300800-75305400	Weak transcription	GM12878-XiMat	blood
3	chr16:75300800-75305800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr16:75301000-75305800	Weak transcription	Adipose Nuclei	Adipose
5	chr16:75301000-75325000	Weak transcription	Liver	Liver
6	chr16:75301200-75305600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:75301600-75305600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:75301800-75305600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:75301800-75305800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr16:75301800-75306000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr16:75301800-75321800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:75302000-75306000	Weak transcription	Right Atrium	heart
13	chr16:75302000-75315800	Weak transcription	Fetal Brain Female	brain
14	chr16:75302000-75324000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr16:75302200-75305600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr16:75302200-75305800	Weak transcription	Spleen	Spleen
17	chr16:75302200-75307400	Weak transcription	Osteobl	bone
18	chr16:75302400-75305400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr16:75302400-75305400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr16:75302400-75305400	Weak transcription	HSMMtube	muscle
21	chr16:75302400-75305600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr16:75302400-75305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr16:75302400-75305600	Weak transcription	NHLF	lung
24	chr16:75302400-75305800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr16:75302400-75305800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr16:75302400-75305800	Weak transcription	Left Ventricle	heart
27	chr16:75302400-75305800	Weak transcription	Psoas Muscle	Psoas
28	chr16:75302400-75305800	Weak transcription	HUVEC	blood vessel
29	chr16:75302400-75306000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr16:75302400-75306000	Weak transcription	A549	lung
31	chr16:75302400-75306200	Weak transcription	NH-A	brain
32	chr16:75302400-75306800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr16:75302400-75306800	Weak transcription	HMEC	breast
34	chr16:75302400-75307000	Weak transcription	NHEK	skin
35	chr16:75302400-75307200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr16:75302400-75307200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr16:75302400-75307400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr16:75302400-75313400	Weak transcription	HSMM	muscle
39	chr16:75302400-75314600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:75302600-75305400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr16:75302600-75305600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr16:75302600-75305800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr16:75302600-75313400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr16:75303400-75305400	Enhancers	HepG2	liver
45	chr16:75303800-75305600	Weak transcription	Fetal Heart	heart
46	chr16:75303800-75305800	Weak transcription	Fetal Lung	lung
47	chr16:75303800-75305800	Weak transcription	Pancreas	Pancrea
48	chr16:75303800-75306000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr16:75303800-75306000	Weak transcription	Hela-S3	cervix
50	chr16:75303800-75306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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