Variant report

Variant	rs28379831
Chromosome Location	chr1:153607631-153607632
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:18)
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	GTF3C2	chr1:153607081-153607692	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:153607483-153608102	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr1:153607385-153607717	HepG2	liver:	n/a	n/a
4	MXI1	chr1:153605489-153608251	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153607617-153607667	PrEC	prostate:	n/a
2	chr1:153607617-153607667	GM06990	blood:	n/a
3	chr1:153607617-153607667	U87	brain:	n/a
4	chr1:153607617-153607667	HL-60	blood:	n/a
5	chr1:153607617-153607667	GM12892	blood:	n/a
6	chr1:153607617-153607667	IMR90	lung:	fetal
7	chr1:153607617-153607667	BE2_C	brain:	n/a
8	chr1:153607617-153607667	NHDF-neo	bronchial:	n/a
9	chr1:153607617-153607667	HPAEpiC	pulmonary alveolar:	n/a
10	chr1:153607617-153607667	CMK	blood:	n/a
11	chr1:153607617-153607667	HEK293	kidney:	embryo
12	chr1:153607617-153607667	ovcar-3	ovarian:	n/a
13	chr1:153607617-153607667	MCF-7	breast:	n/a
14	chr1:153607617-153607667	AG09319	gingival:	n/a
15	chr1:153607617-153607667	GM12891	blood:	n/a
16	chr1:153607617-153607667	MCF10A-Er-Src	breast:	n/a
17	chr1:153607617-153607667	RPTEC	kidney:	n/a
18	chr1:153607617-153607667	ProgFib	skin:	n/a
19	chr1:153607617-153607667	SK-N-SH	brain:	n/a
20	chr1:153607617-153607667	HCT-116	colon:	n/a
21	chr1:153607617-153607667	AG04449	skin:	fetal
22	chr1:153607617-153607667	LNCaP	prostate:	n/a
23	chr1:153607617-153607667	HEEpiC	esophagus:	n/a
24	chr1:153607617-153607667	SK-N-MC	brain:	n/a
25	chr1:153607617-153607667	HUVEC	blood vessel:	n/a
26	chr1:153607617-153607667	Caco-2	colon:	n/a
27	chr1:153607617-153607667	GM12878	blood:	n/a
28	chr1:153607617-153607667	HRPEpiC	eye:	n/a
29	chr1:153607617-153607667	Hepatocyte	liver:	n/a
30	chr1:153607617-153607667	Hela-S3	cervix:	n/a
31	chr1:153607617-153607667	Jurkat	blood:	n/a
32	chr1:153607617-153607667	SKMC	muscle:	n/a
33	chr1:153607617-153607667	HCM	heart:	n/a
34	chr1:153607617-153607667	PFSK-1	brain:	n/a
35	chr1:153607617-153607667	HIPEpiC	eye:	n/a
36	chr1:153607617-153607667	HRE	kidney:	n/a
37	chr1:153607617-153607667	SAEC	small airway:	n/a
38	chr1:153607617-153607667	ECC-1	luminal epithelium:	n/a
39	chr1:153607617-153607667	HRCEpiC	kidney:	n/a
40	chr1:153607617-153607667	NHBE	bronchial:	n/a
41	chr1:153607617-153607667	HCF	heart:	n/a
42	chr1:153607617-153607667	AG10803	skin:	n/a
43	chr1:153607617-153607667	HNPCEpiC	eye:	n/a
44	chr1:153607617-153607667	K562	blood:	n/a
45	chr1:153607617-153607667	NB4	blood:	n/a
46	chr1:153607617-153607667	AG09309	skin:	n/a
47	chr1:153607617-153607667	HepG2	liver:	n/a
48	chr1:153607617-153607667	GM19239	blood:	n/a
49	chr1:153607617-153607667	AoSMC	blood vessel:	n/a
50	chr1:153607617-153607667	A549	lung:	n/a

(count:18 , 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	chr1:153605481..153608017-chr1:153747130..153748871,2	MCF-7	breast:
5	chr1:153605802..153608148-chr1:153700322..153702139,2	K562	blood:
6	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
7	chr1:153605524..153607926-chr1:154955146..154957137,2	K562	blood:
8	chr1:153604957..153607992-chr1:153642564..153646231,5	MCF-7	breast:
9	chr1:153507230..153509062-chr1:153605925..153607769,2	MCF-7	breast:
10	chr1:153504329..153507150-chr1:153606463..153608211,3	MCF-7	breast:
11	chr1:152008592..152010631-chr1:153605290..153607916,2	MCF-7	breast:
12	chr1:153605540..153608540-chr1:153937612..153940414,3	MCF-7	breast:
13	chr1:153605696..153608522-chr1:153629929..153633320,6	MCF-7	breast:
14	chr1:153508630..153510790-chr1:153606132..153607908,2	K562	blood:
15	chr1:153603477..153607903-chr1:153962238..153965498,5	K562	blood:
16	chr1:153604949..153608172-chr1:153935177..153937108,3	K562	blood:
17	chr1:153604928..153608647-chr1:153747112..153750594,4	MCF-7	breast:
18	chr1:153606484..153608148-chr1:153700201..153701822,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272030	TF binding region
CHTOP	TF binding region
S100A13	TF binding region
ENSG00000271853	TF binding region
ENSG00000271853	CpG island
S100A13	CpG island
CHTOP	CpG island
ENSG00000272030	CpG island
ENSG00000143554	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000160688	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000143578	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1046381	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10797056	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797090	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265633	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1128894	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11548103	0.82[EUR][1000 genomes]
rs11548104	0.82[EUR][1000 genomes]
rs11580122	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12139953	0.85[ASN][1000 genomes]
rs12564925	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730186	0.88[ASN][1000 genomes]
rs1411273	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1810836	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1888115	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28380060	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28416529	0.85[EUR][1000 genomes]
rs28510471	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28518786	0.93[ASN][1000 genomes]
rs28580554	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28613361	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28700217	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3790411	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3790412	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795396	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3806233	0.80[ASN][1000 genomes]
rs3806234	0.83[ASN][1000 genomes]
rs3818632	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828031	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862047	0.80[ASN][1000 genomes]
rs4351684	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845557	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845558	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845560	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845563	0.85[ASN][1000 genomes]
rs6427640	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66721814	0.85[ASN][1000 genomes]
rs6694006	0.82[AMR][1000 genomes]
rs7345	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7934	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913860	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs913861	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9330299	0.82[EUR][1000 genomes]
rs9330300	0.82[EUR][1000 genomes]
rs9330301	0.83[EUR][1000 genomes]
rs9661993	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9729773	0.82[EUR][1000 genomes]
rs985242	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs999418	0.81[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28379831	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs28379831	RP1-178F15.4	cis	Artery Aorta	GTEx
rs28379831	CHTOP	cis	Muscle Skeletal	GTEx
rs28379831	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs28379831	RP1-178F15.4	cis	lung	GTEx
rs28379831	S100A13	cis	Adipose Subcutaneous	GTEx
rs28379831	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs28379831	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs28379831	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx
rs28379831	RP1-178F15.4	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153605800-153607800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:153605800-153608000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:153605800-153608000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:153605800-153608000	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr1:153605800-153608200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:153606000-153607800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:153606000-153607800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:153606000-153607800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:153606000-153607800	Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr1:153606000-153607800	Active TSS	Brain Germinal Matrix	brain
11	chr1:153606000-153607800	Active TSS	Fetal Brain Female	brain
12	chr1:153606000-153608000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:153606000-153608200	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr1:153606000-153608400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:153606000-153608400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:153606000-153608400	Active TSS	Psoas Muscle	Psoas
17	chr1:153606000-153608400	Active TSS	A549	lung
18	chr1:153606000-153608400	Active TSS	HSMM	muscle
19	chr1:153606000-153608600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:153606000-153608600	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr1:153606200-153607800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:153606200-153607800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:153606200-153607800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:153606200-153607800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr1:153606200-153607800	Active TSS	Fetal Kidney	kidney
26	chr1:153606200-153607800	Active TSS	Left Ventricle	heart
27	chr1:153606200-153607800	Active TSS	Lung	lung
28	chr1:153606200-153607800	Active TSS	NH-A	brain
29	chr1:153606200-153607800	Active TSS	NHDF-Ad	bronchial
30	chr1:153606200-153607800	Active TSS	NHEK	skin
31	chr1:153606200-153608000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:153606200-153608000	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr1:153606200-153608000	Active TSS	Brain Angular Gyrus	brain
34	chr1:153606200-153608000	Active TSS	Brain Anterior Caudate	brain
35	chr1:153606200-153608000	Active TSS	Fetal Intestine Large	intestine
36	chr1:153606200-153608200	Active TSS	Brain Hippocampus Middle	brain
37	chr1:153606200-153608200	Active TSS	Colon Smooth Muscle	Colon
38	chr1:153606200-153608200	Active TSS	Esophagus	oesophagus
39	chr1:153606200-153608200	Active TSS	Gastric	stomach
40	chr1:153606200-153608200	Active TSS	HMEC	breast
41	chr1:153606200-153608200	Active TSS	K562	blood
42	chr1:153606200-153608200	Active TSS	Osteobl	bone
43	chr1:153606200-153608400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:153606200-153608400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr1:153606200-153608400	Active TSS	Brain Substantia Nigra	brain
46	chr1:153606200-153608400	Active TSS	Right Ventricle	heart
47	chr1:153606200-153608400	Active TSS	NHLF	lung
48	chr1:153606200-153608800	Active TSS	HSMMtube	muscle
49	chr1:153606400-153607800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:153606400-153607800	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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