Variant report

Variant	rs28782525
Chromosome Location	chr1:93708745-93708746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93702441..93705193-chr1:93708597..93710814,3	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10874766	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164885	0.89[ASN][1000 genomes]
rs11164896	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11164905	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12027142	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12030843	0.89[ASN][1000 genomes]
rs12031709	0.80[ASN][1000 genomes]
rs12031765	0.89[ASN][1000 genomes]
rs12033147	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12036057	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12038046	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12044557	0.89[ASN][1000 genomes]
rs12045001	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046063	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12048219	0.90[ASN][1000 genomes]
rs12405487	0.82[ASN][1000 genomes]
rs12563709	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255722	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2391251	0.82[ASN][1000 genomes]
rs2484486	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2783490	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2783493	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2783495	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2783496	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2783497	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2783505	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2815406	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2893242	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087457	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3904665	0.89[ASN][1000 genomes]
rs3904666	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484937	0.87[ASN][1000 genomes]
rs58354545	0.89[ASN][1000 genomes]
rs61799470	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61799497	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61799500	0.89[ASN][1000 genomes]
rs61799516	0.82[ASN][1000 genomes]
rs61799517	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61799538	0.90[ASN][1000 genomes]
rs6676902	0.82[ASN][1000 genomes]
rs6684908	0.82[ASN][1000 genomes]
rs72959220	0.89[ASN][1000 genomes]
rs771454	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs771461	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs771465	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs771476	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs771479	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs771482	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs810027	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28782525	DR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:93682400-93708800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:93685600-93709200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:93688200-93714800	Weak transcription	HSMMtube	muscle
7	chr1:93690400-93729400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
9	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:93693400-93709200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:93703600-93709200	Weak transcription	Fetal Heart	heart
12	chr1:93704200-93729800	Weak transcription	Hela-S3	cervix
13	chr1:93704800-93710800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:93705200-93709000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:93705400-93709000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:93705400-93709400	ZNF genes & repeats	Dnd41	blood
17	chr1:93706200-93710200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
18	chr1:93706400-93709600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:93706400-93727000	Weak transcription	K562	blood
20	chr1:93706600-93709200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
21	chr1:93706600-93710000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
22	chr1:93706600-93710000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
23	chr1:93706600-93710200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr1:93706600-93710200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
25	chr1:93706600-93717200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:93706800-93709600	Strong transcription	Primary T cells from cord blood	blood
27	chr1:93706800-93710200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:93707000-93727400	Weak transcription	Liver	Liver
29	chr1:93707200-93708800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:93707200-93709400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
31	chr1:93707200-93710000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr1:93707400-93708800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:93707400-93709200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
34	chr1:93707400-93709200	ZNF genes & repeats	GM12878-XiMat	blood
35	chr1:93707400-93709400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
36	chr1:93707400-93709400	Strong transcription	A549	lung
37	chr1:93707400-93709600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:93707400-93709600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:93707400-93709800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
40	chr1:93707600-93709600	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:93707600-93709600	ZNF genes & repeats	Primary B cells from cord blood	blood
42	chr1:93707600-93709600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr1:93707600-93709600	ZNF genes & repeats	NHEK	skin
44	chr1:93707800-93709000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:93707800-93709000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
46	chr1:93707800-93709000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:93707800-93709200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:93707800-93709200	ZNF genes & repeats	Fetal Stomach	stomach
49	chr1:93707800-93709200	ZNF genes & repeats	Thymus	Thymus
50	chr1:93707800-93709400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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