Variant report

Variant	rs28518786
Chromosome Location	chr1:153608116-153608117
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153608010-153608173	MCF-7	breast:	n/a	n/a
2	MAX	chr1:153607816-153608240	K562	blood:	n/a	n/a
3	POLR2A	chr1:153607934-153608328	HepG2	liver:	n/a	n/a
4	MXI1	chr1:153605489-153608251	SK-N-SH	brain:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153605618..153608356-chr1:153961854..153964729,2	MCF-7	breast:
2	chr1:153607039..153609365-chr1:153641782..153643312,2	K562	blood:
3	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
4	chr1:153605802..153608148-chr1:153700322..153702139,2	K562	blood:
5	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
6	chr1:153504329..153507150-chr1:153606463..153608211,3	MCF-7	breast:
7	chr1:153605540..153608540-chr1:153937612..153940414,3	MCF-7	breast:
8	chr1:153605696..153608522-chr1:153629929..153633320,6	MCF-7	breast:
9	chr1:153604949..153608172-chr1:153935177..153937108,3	K562	blood:
10	chr1:153604928..153608647-chr1:153747112..153750594,4	MCF-7	breast:
11	chr1:153606484..153608148-chr1:153700201..153701822,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271853	TF binding region
S100A13	TF binding region
CHTOP	TF binding region
ENSG00000272030	TF binding region
ENSG00000196754	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000143553	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1046381	0.92[ASN][1000 genomes]
rs10797056	0.93[ASN][1000 genomes]
rs10797090	0.86[ASN][1000 genomes]
rs10797096	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10908746	0.93[ASN][1000 genomes]
rs10908848	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11265625	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1128894	0.89[ASN][1000 genomes]
rs11548102	0.89[EUR][1000 genomes]
rs11580122	0.89[ASN][1000 genomes]
rs11588347	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12139953	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12564925	0.93[ASN][1000 genomes]
rs12730186	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1888115	0.91[ASN][1000 genomes]
rs2274739	0.93[ASN][1000 genomes]
rs2274740	0.93[ASN][1000 genomes]
rs28379831	0.93[ASN][1000 genomes]
rs28380060	0.92[ASN][1000 genomes]
rs28416529	0.81[ASN][1000 genomes]
rs28510471	0.86[ASN][1000 genomes]
rs28580554	0.92[ASN][1000 genomes]
rs28613361	0.86[ASN][1000 genomes]
rs28700217	0.92[ASN][1000 genomes]
rs28754733	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35760493	0.81[ASN][1000 genomes]
rs3790411	0.84[ASN][1000 genomes]
rs3790412	0.92[ASN][1000 genomes]
rs3806233	0.89[EUR][1000 genomes]
rs3806234	0.87[ASN][1000 genomes]
rs3818632	0.91[ASN][1000 genomes]
rs3828031	0.92[ASN][1000 genomes]
rs3862047	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4072425	0.89[EUR][1000 genomes]
rs4845557	0.93[ASN][1000 genomes]
rs4845558	0.81[ASN][1000 genomes]
rs4845563	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845564	0.94[EUR][1000 genomes]
rs55772653	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6427640	0.81[ASN][1000 genomes]
rs66721814	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6674929	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7345	0.80[ASN][1000 genomes]
rs7934	0.90[ASN][1000 genomes]
rs913861	0.89[ASN][1000 genomes]
rs9330298	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9330301	0.81[ASN][1000 genomes]
rs9662664	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9700928	0.86[EUR][1000 genomes]
rs9726753	0.89[EUR][1000 genomes]
rs9792913	0.82[EUR][1000 genomes]
rs9792963	0.89[EUR][1000 genomes]
rs9792967	0.89[EUR][1000 genomes]
rs999418	0.81[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
rs28518786	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx
rs28518786	S100A13	cis	Adipose Subcutaneous	GTEx
rs28518786	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs28518786	CHTOP	cis	Muscle Skeletal	GTEx
rs28518786	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs28518786	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs28518786	S100A16	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153605800-153608200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:153606000-153608200	Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr1:153606000-153608400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:153606000-153608400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:153606000-153608400	Active TSS	Psoas Muscle	Psoas
6	chr1:153606000-153608400	Active TSS	A549	lung
7	chr1:153606000-153608400	Active TSS	HSMM	muscle
8	chr1:153606000-153608600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:153606000-153608600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:153606200-153608200	Active TSS	Brain Hippocampus Middle	brain
11	chr1:153606200-153608200	Active TSS	Colon Smooth Muscle	Colon
12	chr1:153606200-153608200	Active TSS	Esophagus	oesophagus
13	chr1:153606200-153608200	Active TSS	Gastric	stomach
14	chr1:153606200-153608200	Active TSS	HMEC	breast
15	chr1:153606200-153608200	Active TSS	K562	blood
16	chr1:153606200-153608200	Active TSS	Osteobl	bone
17	chr1:153606200-153608400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:153606200-153608400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr1:153606200-153608400	Active TSS	Brain Substantia Nigra	brain
20	chr1:153606200-153608400	Active TSS	Right Ventricle	heart
21	chr1:153606200-153608400	Active TSS	NHLF	lung
22	chr1:153606200-153608800	Active TSS	HSMMtube	muscle
23	chr1:153606400-153608200	Active TSS	Muscle Satellite Cultured Cells	--
24	chr1:153606400-153608200	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:153606400-153608200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr1:153606400-153608200	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr1:153606400-153608400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:153606400-153608400	Active TSS	Ovary	ovary
29	chr1:153606400-153608400	Active TSS	Pancreas	Pancrea
30	chr1:153606400-153608400	Active TSS	GM12878-XiMat	blood
31	chr1:153606400-153608400	Active TSS	Hela-S3	cervix
32	chr1:153606800-153608400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:153606800-153608400	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr1:153607000-153608200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:153607200-153608200	Weak transcription	Stomach Mucosa	stomach
36	chr1:153607200-153608600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:153607200-153610200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:153607400-153608200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr1:153607400-153608200	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr1:153607400-153608400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr1:153607400-153609000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:153607600-153608200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:153607600-153608200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:153607600-153608200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:153607600-153608200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr1:153607600-153608200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
47	chr1:153607600-153608400	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr1:153607600-153608400	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr1:153607600-153608400	Flanking Active TSS	Placenta	Placenta
50	chr1:153607600-153608600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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