Variant report

Variant	rs28575168
Chromosome Location	chr1:75187963-75187964
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75184634..75186342-chr1:75186359..75187995,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11162945	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1122338	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1133891	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11485264	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11485299	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12034724	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12043726	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13375787	0.82[AMR][1000 genomes]
rs1359750	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1581870	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2032969	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28374065	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28436025	0.82[AMR][1000 genomes]
rs28445096	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28515016	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28563168	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28719150	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28740807	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28804147	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28810187	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806161	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3819946	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3819947	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4650004	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4650007	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4650287	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4650288	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58715708	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60292279	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6681874	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67696801	0.82[AMR][1000 genomes]
rs745108	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7535692	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7540514	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs768223	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv871152	chr1:75152186-75197533	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28575168	TYW3	cis	Artery Tibial	GTEx
rs28575168	TYW3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75166400-75191400	Weak transcription	Placenta	Placenta
2	chr1:75166600-75194800	Weak transcription	Esophagus	oesophagus
3	chr1:75166800-75189200	Weak transcription	Spleen	Spleen
4	chr1:75167000-75197200	Weak transcription	Right Ventricle	heart
5	chr1:75167600-75190600	Strong transcription	Liver	Liver
6	chr1:75167600-75190800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:75167800-75190000	Strong transcription	Adipose Nuclei	Adipose
8	chr1:75169000-75189600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:75169400-75190600	Strong transcription	Primary B cells from cord blood	blood
10	chr1:75169400-75191600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:75169800-75191800	Weak transcription	Colonic Mucosa	Colon
12	chr1:75170400-75189600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:75171000-75197200	Weak transcription	Brain Angular Gyrus	brain
14	chr1:75171800-75189800	Strong transcription	HepG2	liver
15	chr1:75172000-75189400	Strong transcription	Fetal Muscle Leg	muscle
16	chr1:75173400-75189200	Strong transcription	Ovary	ovary
17	chr1:75173400-75189600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:75173600-75189600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:75174600-75189600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr1:75174800-75198000	Weak transcription	Thymus	Thymus
21	chr1:75175400-75196000	Weak transcription	HSMMtube	muscle
22	chr1:75176400-75189400	Strong transcription	Primary T cells from cord blood	blood
23	chr1:75176600-75189600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:75176800-75191600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:75177400-75188800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:75177400-75191600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:75177400-75191600	Weak transcription	Gastric	stomach
28	chr1:75177400-75191800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:75178000-75191800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:75178800-75189400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:75179000-75189600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:75179000-75189800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:75179200-75189600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:75179400-75191200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:75179600-75189800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:75179600-75191200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:75179800-75189400	Strong transcription	Left Ventricle	heart
38	chr1:75179800-75191600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:75179800-75191600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:75180000-75191000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:75180000-75196000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:75180200-75188400	Strong transcription	K562	blood
43	chr1:75180400-75189800	Strong transcription	Fetal Lung	lung
44	chr1:75180400-75191000	Strong transcription	A549	lung
45	chr1:75180400-75197200	Weak transcription	Psoas Muscle	Psoas
46	chr1:75180600-75191200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:75180800-75190800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:75180800-75190800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:75180800-75190800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:75181000-75189800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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