Variant report

Variant	rs1411273
Chromosome Location	chr1:153602435-153602436
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153602351-153603190	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:153602387-153603021	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153602112..153603673-chr1:153935827..153937961,2	K562	blood:
2	chr1:153511330..153514182-chr1:153601360..153604176,2	K562	blood:
3	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
4	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
5	chr1:153508608..153510769-chr1:153600428..153603319,2	K562	blood:
6	chr1:153601533..153603060-chr1:153962861..153964881,2	K562	blood:
7	chr1:153537973..153540755-chr1:153602282..153604926,2	K562	blood:
8	chr1:153601528..153604004-chr1:153917956..153919645,2	MCF-7	breast:
9	chr1:153598392..153603036-chr1:153933813..153937554,5	MCF-7	breast:
10	chr1:153601860..153603446-chr1:153642030..153643721,2	MCF-7	breast:

No data

Variant related genes	Relation type
CHTOP	TF binding region
S100A13	TF binding region
ENSG00000197956	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000196420	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000177954	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1046381	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10797056	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10908746	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1128894	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11497739	0.87[EUR][1000 genomes]
rs11548103	0.93[EUR][1000 genomes]
rs11548104	0.93[EUR][1000 genomes]
rs12564925	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1810836	0.80[EUR][1000 genomes]
rs1888115	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2274739	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2274740	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28379831	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28380060	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28416529	0.95[EUR][1000 genomes]
rs28580554	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28700217	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3790411	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3790412	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3818632	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3828031	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4845557	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7934	0.80[EUR][1000 genomes]
rs913860	0.80[EUR][1000 genomes]
rs913861	0.81[EUR][1000 genomes]
rs9330299	0.93[EUR][1000 genomes]
rs9330300	0.92[EUR][1000 genomes]
rs9330301	0.94[EUR][1000 genomes]
rs9660679	0.86[EUR][1000 genomes]
rs9729773	0.93[EUR][1000 genomes]
rs9793310	0.85[EUR][1000 genomes]
rs985242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs999418	0.90[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1411273	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs1411273	CHTOP	cis	Muscle Skeletal	GTEx
rs1411273	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs1411273	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs1411273	S100A14	cis	Esophagus Mucosa	GTEx
rs1411273	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153598200-153603600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr1:153600000-153602600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:153600000-153602600	Enhancers	Fetal Thymus	thymus
4	chr1:153600000-153603200	Enhancers	Lung	lung
5	chr1:153600000-153604200	Enhancers	Fetal Heart	heart
6	chr1:153600000-153605600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:153600000-153605800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:153600000-153605800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:153600000-153605800	Weak transcription	Thymus	Thymus
10	chr1:153600000-153606600	Weak transcription	Aorta	Aorta
11	chr1:153600200-153602600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:153600200-153602600	Weak transcription	Gastric	stomach
13	chr1:153600200-153603000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:153600200-153603200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:153600200-153603200	Enhancers	Adipose Nuclei	Adipose
16	chr1:153600200-153603400	Weak transcription	Liver	Liver
17	chr1:153600200-153603600	Enhancers	Fetal Stomach	stomach
18	chr1:153600200-153603800	Enhancers	Fetal Muscle Leg	muscle
19	chr1:153600200-153604200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:153600200-153604200	Enhancers	HSMMtube	muscle
21	chr1:153600200-153604400	Enhancers	Placenta	Placenta
22	chr1:153600200-153605800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:153600200-153606000	Enhancers	Fetal Intestine Small	intestine
24	chr1:153600400-153602600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:153600400-153602800	Weak transcription	Fetal Lung	lung
26	chr1:153600400-153603000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:153600400-153603200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:153600400-153603200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:153600400-153603200	Enhancers	Fetal Muscle Trunk	muscle
30	chr1:153600400-153603600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:153600400-153605800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:153600400-153605800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:153600400-153605800	Weak transcription	HUVEC	blood vessel
34	chr1:153600400-153606000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:153600400-153606000	Weak transcription	Fetal Brain Male	brain
36	chr1:153600400-153606000	Enhancers	Fetal Intestine Large	intestine
37	chr1:153600400-153606400	Weak transcription	Small Intestine	intestine
38	chr1:153600600-153603000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:153600600-153603600	Weak transcription	NHLF	lung
40	chr1:153600600-153603800	Weak transcription	NH-A	brain
41	chr1:153600600-153605600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:153600600-153605600	Weak transcription	NHDF-Ad	bronchial
43	chr1:153600600-153605800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:153600600-153605800	Weak transcription	GM12878-XiMat	blood
45	chr1:153600800-153603200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:153600800-153603400	Weak transcription	Colonic Mucosa	Colon
47	chr1:153600800-153603600	Weak transcription	Stomach Mucosa	stomach
48	chr1:153600800-153605000	Weak transcription	Hela-S3	cervix
49	chr1:153600800-153605200	Weak transcription	Pancreas	Pancrea
50	chr1:153600800-153605600	Weak transcription	Colon Smooth Muscle	Colon

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