Variant report

Variant	rs35760493
Chromosome Location	chr1:153596603-153596604
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	STAT3	chr1:153596553-153596650	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153541191..153544684-chr1:153594586..153597033,3	MCF-7	breast:
2	chr1:153539227..153541131-chr1:153594881..153597093,2	MCF-7	breast:
3	chr1:153527411..153530387-chr1:153595127..153597966,2	MCF-7	breast:

Variant related genes	Relation type
S100A1	TF binding region
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1046381	0.85[ASN][1000 genomes]
rs11497739	0.94[ASN][1000 genomes]
rs11548102	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548103	0.95[ASN][1000 genomes]
rs11548104	0.95[ASN][1000 genomes]
rs28416529	0.97[ASN][1000 genomes]
rs28518786	0.81[ASN][1000 genomes]
rs28754733	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806233	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4072425	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330298	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330299	0.95[ASN][1000 genomes]
rs9330300	0.94[ASN][1000 genomes]
rs9330301	0.97[ASN][1000 genomes]
rs9660679	0.94[ASN][1000 genomes]
rs9699949	0.95[ASN][1000 genomes]
rs9700179	0.94[ASN][1000 genomes]
rs9700928	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9726753	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9729773	0.97[ASN][1000 genomes]
rs9792913	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9792963	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9792967	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9793310	0.94[ASN][1000 genomes]
rs999418	0.97[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
rs35760493	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs35760493	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs35760493	RP1-178F15.4	cis	Thyroid	GTEx
rs35760493	S100A14	cis	Esophagus Mucosa	GTEx
rs35760493	CHTOP	cis	Muscle Skeletal	GTEx
rs35760493	S100A16	cis	Muscle Skeletal	GTEx
rs35760493	RP1-178F15.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153585600-153597600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:153585600-153598800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:153585600-153599000	Weak transcription	Aorta	Aorta
4	chr1:153585800-153599200	Weak transcription	Fetal Brain Male	brain
5	chr1:153586000-153598800	Weak transcription	Psoas Muscle	Psoas
6	chr1:153588600-153598800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:153589200-153599400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:153589400-153598600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:153589600-153597800	Weak transcription	HepG2	liver
10	chr1:153590000-153598600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:153590400-153597800	Weak transcription	Right Atrium	heart
12	chr1:153590400-153598200	Weak transcription	Colonic Mucosa	Colon
13	chr1:153590400-153598200	Weak transcription	Pancreas	Pancrea
14	chr1:153590400-153598600	Weak transcription	Brain Anterior Caudate	brain
15	chr1:153590400-153598600	Weak transcription	Esophagus	oesophagus
16	chr1:153590400-153598600	Weak transcription	Gastric	stomach
17	chr1:153590400-153598600	Weak transcription	K562	blood
18	chr1:153590600-153598000	Weak transcription	Small Intestine	intestine
19	chr1:153590600-153598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:153590600-153599400	Weak transcription	Primary B cells from cord blood	blood
21	chr1:153590800-153598800	Weak transcription	Stomach Mucosa	stomach
22	chr1:153591000-153598800	Strong transcription	Fetal Intestine Small	intestine
23	chr1:153591200-153596800	Strong transcription	HMEC	breast
24	chr1:153591200-153598000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:153592200-153597200	Weak transcription	Lung	lung
26	chr1:153592400-153598000	Weak transcription	Ovary	ovary
27	chr1:153592400-153598000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:153592400-153598200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:153592800-153596800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:153593400-153596800	Weak transcription	NHEK	skin
31	chr1:153593400-153598600	Weak transcription	Fetal Lung	lung
32	chr1:153594800-153597000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:153594800-153597800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:153594800-153598000	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:153594800-153598200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:153595000-153596800	Strong transcription	HUVEC	blood vessel
37	chr1:153595000-153597000	Genic enhancers	Rectal Smooth Muscle	rectum
38	chr1:153595000-153597200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr1:153595000-153598200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:153595000-153598400	Genic enhancers	Adipose Nuclei	Adipose
41	chr1:153595000-153598400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr1:153595200-153596800	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr1:153595200-153597600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:153595200-153598000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:153595600-153596800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:153595600-153597200	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr1:153595600-153598200	Strong transcription	Fetal Intestine Large	intestine
48	chr1:153595600-153598200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:153595800-153598000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:153595800-153598200	Weak transcription	A549	lung

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