Variant report

Variant	rs28365978
Chromosome Location	chr1:160990878-160990879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160989106..160992104-chr1:161101728..161103686,4	K562	blood:
2	chr1:160989693..160991522-chr1:161127596..161130418,2	MCF-7	breast:
3	chr1:160990808..160991668-chr11:85780243..85780839,2	HCT-116	colon:
4	chr1:160988929..160992185-chr1:161012707..161018170,8	MCF-7	breast:
5	chr1:160989498..160991645-chr1:161056781..161059472,2	MCF-7	breast:
6	chr1:160989661..160992673-chr1:161066595..161070388,4	K562	blood:
7	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:
8	chr1:160990576..160992373-chr1:161014612..161018487,6	K562	blood:
9	chr1:160989097..160992016-chr1:161278410..161280382,2	K562	blood:
10	chr1:160990813..160992339-chr17:57183553..57186254,2	MCF-7	breast:
11	chr1:160987801..160992609-chr1:161065993..161069595,4	MCF-7	breast:
12	chr1:160989787..160992592-chr1:161127591..161130267,2	K562	blood:
13	chr1:160989864..160992775-chr1:161169949..161172743,2	MCF-7	breast:
14	chr1:160989663..160992818-chr1:161011844..161017868,15	MCF-7	breast:
15	chr1:160988368..160992141-chr1:161085559..161090183,5	MCF-7	breast:
16	chr1:160990492..160992160-chr1:161130814..161132595,2	K562	blood:
17	chr1:160989721..160993044-chr1:161014364..161019082,7	K562	blood:
18	chr1:160638640..160640892-chr1:160989316..160991533,2	K562	blood:
19	chr1:45187018..45187769-chr1:160990629..160991569,2	NB4	blood:
20	chr1:160988859..160991431-chr1:161086289..161089011,2	K562	blood:
21	chr1:160989661..160992673-chr1:161067559..161070388,3	K562	blood:
22	chr1:160987861..160992104-chr1:161101436..161104060,5	K562	blood:
23	chr1:160990864..160991491-chr17:3571321..3572276,2	Hela-S3	cervix:
24	chr1:160989495..160995605-chr1:161004888..161010340,15	MCF-7	breast:
25	chr1:160990538..160991527-chr6:74230337..74231147,2	Hela-S3	cervix:
26	chr1:160988819..160994033-chr1:161005548..161011188,8	MCF-7	breast:
27	chr1:160989087..160991942-chr1:161007144..161014242,6	K562	blood:
28	chr1:160990711..160991608-chr1:161008481..161009243,2	MCF-7	breast:
29	chr1:160989601..160993379-chr1:161101301..161104263,5	MCF-7	breast:
30	chr1:160990569..160991458-chr6:86388051..86388956,2	HCT-116	colon:

No data

Variant related genes	Relation type
ENSG00000270149	Chromatin interaction
ENSG00000213977	Chromatin interaction
ENSG00000235101	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000127774	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000143217	Chromatin interaction
ENSG00000143258	Chromatin interaction
ENSG00000158887	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000228863	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000073921	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000224985	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000158864	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12030262	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12723902	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12743772	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2243479	0.82[ASN][1000 genomes]
rs2250288	0.87[ASN][1000 genomes]
rs2481072	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2483143	0.85[ASN][1000 genomes]
rs2483144	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2483148	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2988723	0.87[ASN][1000 genomes]
rs2990700	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2990701	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2990704	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2990705	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007156	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007157	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656975	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530765	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7546890	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427367	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28365978	F11R	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160984400-160991000	Weak transcription	HSMM	muscle
2	chr1:160988000-160992000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:160988400-160991800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:160988400-160991800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:160988400-160991800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:160988600-160991200	Active TSS	Esophagus	oesophagus
7	chr1:160988600-160992000	Active TSS	H1 Cell Line	embryonic stem cell
8	chr1:160988600-160992200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:160988800-160991000	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr1:160988800-160991800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:160988800-160991800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr1:160988800-160991800	Active TSS	Colonic Mucosa	Colon
13	chr1:160988800-160992000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr1:160989000-160991400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:160989000-160991400	Active TSS	NHEK	skin
16	chr1:160989000-160991600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:160989000-160991800	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr1:160989000-160992000	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:160989000-160992000	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr1:160989200-160991800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:160989400-160991400	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:160989400-160991600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:160989400-160991600	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr1:160989400-160991600	Active TSS	Fetal Intestine Small	intestine
25	chr1:160989400-160991600	Active TSS	Right Atrium	heart
26	chr1:160989400-160991800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:160989600-160991000	Active TSS	Brain Substantia Nigra	brain
28	chr1:160989600-160991200	Active TSS	Brain Anterior Caudate	brain
29	chr1:160989600-160991400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:160989600-160991400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr1:160989600-160991400	Active TSS	Stomach Mucosa	stomach
32	chr1:160989600-160991600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr1:160989600-160991600	Active TSS	A549	lung
34	chr1:160989600-160991800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:160989600-160991800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:160989800-160991000	Active TSS	Left Ventricle	heart
37	chr1:160989800-160991200	Active TSS	Small Intestine	intestine
38	chr1:160989800-160991200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
39	chr1:160989800-160991400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:160989800-160991400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:160989800-160991400	Active TSS	HMEC	breast
42	chr1:160989800-160991600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:160989800-160991600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:160989800-160991600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:160989800-160991600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:160989800-160991600	Flanking Active TSS	Fetal Thymus	thymus
47	chr1:160989800-160991600	Active TSS	Gastric	stomach
48	chr1:160989800-160991600	Active TSS	Ovary	ovary
49	chr1:160990000-160991000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:160990000-160991000	Active TSS	Brain Angular Gyrus	brain

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