Variant report

Variant	rs9726753
Chromosome Location	chr1:153591652-153591653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153591555-153591856	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:153591561-153591822	K562	blood:	n/a	n/a
3	POLR2A	chr1:153591060-153591668	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153517680..153519844-chr1:153589905..153591815,2	K562	blood:
2	chr1:153505470..153506193-chr1:153591182..153592078,2	K562	blood:
3	chr1:153567650..153570304-chr1:153590383..153593147,2	K562	blood:

Variant related genes	Relation type
S100A14	TF binding region
ENSG00000238279	Chromatin interaction
ENSG00000196154	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1046381	0.84[ASN][1000 genomes]
rs10797096	0.85[EUR][1000 genomes]
rs10908848	0.83[EUR][1000 genomes]
rs11265625	0.85[EUR][1000 genomes]
rs11497739	0.96[ASN][1000 genomes]
rs11548102	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11548103	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548104	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11588347	0.84[EUR][1000 genomes]
rs12139953	0.83[EUR][1000 genomes]
rs12730186	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28416529	0.96[ASN][1000 genomes]
rs28518786	0.89[EUR][1000 genomes]
rs28754733	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35760493	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35890901	0.81[ASN][1000 genomes]
rs3806233	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3862047	0.85[EUR][1000 genomes]
rs4072425	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845563	0.87[EUR][1000 genomes]
rs4845564	0.84[EUR][1000 genomes]
rs55772653	0.85[EUR][1000 genomes]
rs66721814	0.86[EUR][1000 genomes]
rs6674929	0.83[EUR][1000 genomes]
rs9330298	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9330299	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330300	0.96[ASN][1000 genomes]
rs9330301	0.96[ASN][1000 genomes]
rs9660679	0.96[ASN][1000 genomes]
rs9662664	0.80[EUR][1000 genomes]
rs9699949	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9700179	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9700928	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9729773	0.96[ASN][1000 genomes]
rs9792913	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9792963	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9792967	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793310	0.96[ASN][1000 genomes]
rs999418	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS 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 miRNA target site	236 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9726753	RP1-178F15.4	cis	Thyroid	GTEx
rs9726753	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs9726753	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs9726753	CHTOP	cis	Muscle Skeletal	GTEx
rs9726753	S100A14	cis	Esophagus Mucosa	GTEx
rs9726753	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs9726753	S100A16	cis	Muscle Skeletal	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153585600-153592200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:153585600-153596400	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:153585600-153597600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:153585600-153598800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:153585600-153599000	Weak transcription	Aorta	Aorta
6	chr1:153585800-153599200	Weak transcription	Fetal Brain Male	brain
7	chr1:153586000-153595600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:153586000-153596200	Weak transcription	Fetal Kidney	kidney
9	chr1:153586000-153598800	Weak transcription	Psoas Muscle	Psoas
10	chr1:153588600-153598800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:153589000-153596200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:153589200-153595200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:153589200-153599400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:153589400-153595400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:153589400-153596400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:153589400-153598600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:153589600-153597800	Weak transcription	HepG2	liver
18	chr1:153590000-153592400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:153590000-153598600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:153590200-153592800	Weak transcription	Fetal Intestine Large	intestine
21	chr1:153590200-153593000	Weak transcription	Fetal Lung	lung
22	chr1:153590200-153596200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:153590400-153591800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:153590400-153593400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:153590400-153593400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:153590400-153595000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:153590400-153596200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:153590400-153596200	Strong transcription	Osteobl	bone
29	chr1:153590400-153596400	Weak transcription	Liver	Liver
30	chr1:153590400-153596400	Weak transcription	Right Ventricle	heart
31	chr1:153590400-153596400	Weak transcription	Spleen	Spleen
32	chr1:153590400-153597800	Weak transcription	Right Atrium	heart
33	chr1:153590400-153598200	Weak transcription	Colonic Mucosa	Colon
34	chr1:153590400-153598200	Weak transcription	Pancreas	Pancrea
35	chr1:153590400-153598600	Weak transcription	Brain Anterior Caudate	brain
36	chr1:153590400-153598600	Weak transcription	Esophagus	oesophagus
37	chr1:153590400-153598600	Weak transcription	Gastric	stomach
38	chr1:153590400-153598600	Weak transcription	K562	blood
39	chr1:153590600-153592000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:153590600-153592600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:153590600-153593200	Strong transcription	Adipose Nuclei	Adipose
42	chr1:153590600-153593200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr1:153590600-153593400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:153590600-153593400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr1:153590600-153595000	Weak transcription	HUVEC	blood vessel
46	chr1:153590600-153595200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:153590600-153595200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:153590600-153595200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr1:153590600-153595400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr1:153590600-153596200	Weak transcription	Brain Substantia Nigra	brain

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