Variant report

Variant	rs28700217
Chromosome Location	chr1:153605260-153605261
allele	A/G
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:14)
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	chr1:153604968-153607263	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:153605104-153605292	HepG2	liver:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153603477..153606996-chr1:153962238..153964716,3	K562	blood:
2	chr1:153604905..153607517-chr1:153700319..153703388,3	MCF-7	breast:
3	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
4	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
5	chr1:153604920..153606894-chr1:153640638..153643940,3	K562	blood:
6	chr1:149222274..149224948-chr1:153604341..153607220,2	MCF-7	breast:
7	chr1:153539289..153541606-chr1:153604560..153606747,2	K562	blood:
8	chr1:153603827..153606641-chr1:153939224..153941084,2	MCF-7	breast:
9	chr1:153604957..153607992-chr1:153642564..153646231,5	MCF-7	breast:
10	chr1:153536900..153539436-chr1:153605197..153607603,3	K562	blood:
11	chr1:153603477..153607903-chr1:153962238..153965498,5	K562	blood:
12	chr1:153604905..153606814-chr1:153723152..153725405,2	K562	blood:
13	chr1:153604949..153608172-chr1:153935177..153937108,3	K562	blood:
14	chr1:153604928..153608647-chr1:153747112..153750594,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272030	TF binding region
CHTOP	TF binding region
S100A13	TF binding region
ENSG00000143621	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000243613	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000233222	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1046381	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10797056	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797090	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908746	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265633	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1128894	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11548103	0.82[EUR][1000 genomes]
rs11548104	0.82[EUR][1000 genomes]
rs11580122	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12139953	0.85[ASN][1000 genomes]
rs12564925	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12730186	0.88[ASN][1000 genomes]
rs1411273	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1810836	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1888115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274739	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274740	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28379831	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28380060	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28416529	0.85[EUR][1000 genomes]
rs28510471	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28518786	0.92[ASN][1000 genomes]
rs28580554	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613361	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3790411	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3790412	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795396	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3806233	0.81[ASN][1000 genomes]
rs3806234	0.83[ASN][1000 genomes]
rs3818632	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828031	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4351684	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845557	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4845558	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845560	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845563	0.85[ASN][1000 genomes]
rs6427640	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66721814	0.85[ASN][1000 genomes]
rs6694006	0.81[AMR][1000 genomes]
rs7345	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7934	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs913860	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs913861	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9330299	0.82[EUR][1000 genomes]
rs9330300	0.82[EUR][1000 genomes]
rs9330301	0.83[EUR][1000 genomes]
rs9661993	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9729773	0.82[EUR][1000 genomes]
rs985242	0.80[EUR][1000 genomes];0.83[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
rs28700217	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs28700217	S100A13	cis	Adipose Subcutaneous	GTEx
rs28700217	RP1-178F15.4	cis	Artery Aorta	GTEx
rs28700217	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs28700217	RP1-178F15.4	cis	lung	GTEx
rs28700217	CHTOP	cis	Muscle Skeletal	GTEx
rs28700217	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx
rs28700217	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs28700217	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs28700217	RP1-178F15.4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153600000-153605600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:153600000-153605800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:153600000-153605800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:153600000-153605800	Weak transcription	Thymus	Thymus
5	chr1:153600000-153606600	Weak transcription	Aorta	Aorta
6	chr1:153600200-153605800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:153600200-153606000	Enhancers	Fetal Intestine Small	intestine
8	chr1:153600400-153605800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:153600400-153605800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:153600400-153605800	Weak transcription	HUVEC	blood vessel
11	chr1:153600400-153606000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:153600400-153606000	Weak transcription	Fetal Brain Male	brain
13	chr1:153600400-153606000	Enhancers	Fetal Intestine Large	intestine
14	chr1:153600400-153606400	Weak transcription	Small Intestine	intestine
15	chr1:153600600-153605600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:153600600-153605600	Weak transcription	NHDF-Ad	bronchial
17	chr1:153600600-153605800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:153600600-153605800	Weak transcription	GM12878-XiMat	blood
19	chr1:153600800-153605600	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:153600800-153605600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:153600800-153605600	Weak transcription	NHEK	skin
22	chr1:153600800-153606400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:153601000-153605600	Weak transcription	HMEC	breast
24	chr1:153601200-153605800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:153601200-153606000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:153601400-153605800	Weak transcription	Primary B cells from cord blood	blood
27	chr1:153601400-153605800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:153601400-153606000	Weak transcription	Brain Angular Gyrus	brain
29	chr1:153601600-153605800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:153601600-153606000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:153601800-153605800	Weak transcription	Fetal Kidney	kidney
32	chr1:153602000-153606000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:153602200-153606000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:153602200-153606400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:153602400-153605800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:153602600-153605600	Weak transcription	Esophagus	oesophagus
37	chr1:153602600-153605800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:153602600-153605800	Weak transcription	Fetal Thymus	thymus
39	chr1:153602600-153606000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:153602800-153605800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:153602800-153606400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr1:153603000-153605600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:153603000-153605600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:153603000-153605600	Weak transcription	Gastric	stomach
45	chr1:153603000-153605600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:153603000-153605800	Weak transcription	HSMM	muscle
47	chr1:153603000-153606000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:153603000-153606600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:153603200-153605600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:153603200-153605600	Weak transcription	Fetal Muscle Trunk	muscle

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