Variant report

Variant	rs12408778
Chromosome Location	chr1:160963724-160963725
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:160961010..160963453-chr1:160963698..160966046,2	K562	blood:
2	chr1:160962271..160965107-chr1:160990509..160992689,3	K562	blood:
3	chr1:160960637..160963812-chr1:161007748..161011422,3	K562	blood:
4	chr1:160961592..160964818-chr1:160987864..160991382,4	MCF-7	breast:
5	chr1:160963652..160965235-chr1:161068556..161070373,2	MCF-7	breast:
6	chr1:160962015..160964987-chr1:161100908..161102645,2	K562	blood:
7	chr1:160963683..160965839-chr1:160983750..160985803,2	K562	blood:
8	chr1:160963251..160966052-chr1:160993360..160995980,2	K562	blood:
9	chr1:160962192..160965720-chr1:160976093..160980486,3	MCF-7	breast:
10	chr1:160963404..160964072-chr1:161041337..161041980,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000158769	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000158796	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1044478	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1062826	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1062827	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265540	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11265542	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11799478	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11799521	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11801586	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11805856	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11807930	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12401336	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12405782	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565932	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17388108	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1806774	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2073656	0.82[AMR][1000 genomes]
rs2073658	0.82[AMR][1000 genomes]
rs2243427	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247459	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2247596	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247671	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247790	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251597	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251728	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2297219	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297220	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297221	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2297222	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2481080	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2481081	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2481083	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2481084	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2481085	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2483145	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2774274	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2988726	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3119321	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3737785	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737787	0.80[AMR][1000 genomes]
rs41267947	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41267949	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41267951	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41269993	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4339888	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs61802231	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61803664	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61803665	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61803671	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61803672	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72712854	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs812741	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869985	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	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
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12408778	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160948600-160968000	Weak transcription	Ovary	ovary
2	chr1:160952200-160964400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:160952200-160967000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:160953200-160966600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:160953800-160968200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:160955800-160964400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:160957200-160966800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:160957400-160967000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:160957800-160968000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:160958200-160966600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:160960000-160967200	Weak transcription	Primary B cells from cord blood	blood
12	chr1:160960000-160967400	Weak transcription	Lung	lung
13	chr1:160960000-160968000	Weak transcription	Pancreas	Pancrea
14	chr1:160960000-160970200	Weak transcription	Right Ventricle	heart
15	chr1:160960200-160964600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:160960200-160966800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:160960200-160967000	Weak transcription	Placenta	Placenta
18	chr1:160960200-160967600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:160960200-160967600	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:160960200-160968000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:160960200-160968400	Weak transcription	Left Ventricle	heart
22	chr1:160960400-160966800	Weak transcription	Adipose Nuclei	Adipose
23	chr1:160960400-160967000	Weak transcription	Fetal Intestine Small	intestine
24	chr1:160960400-160967600	Weak transcription	Fetal Stomach	stomach
25	chr1:160960400-160968000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:160960400-160968200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:160960400-160968200	Weak transcription	Fetal Brain Female	brain
28	chr1:160960400-160978400	Weak transcription	Fetal Lung	lung
29	chr1:160960600-160964400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:160960600-160964600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:160960600-160964600	Weak transcription	NHEK	skin
32	chr1:160960600-160964800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:160960600-160965000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:160960600-160965000	Weak transcription	HUVEC	blood vessel
35	chr1:160960600-160965400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:160960600-160966200	Weak transcription	Fetal Intestine Large	intestine
37	chr1:160960600-160966400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:160960600-160966400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:160960600-160966600	Weak transcription	Liver	Liver
40	chr1:160960600-160966800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:160960600-160967000	Weak transcription	Fetal Thymus	thymus
42	chr1:160960600-160967000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:160960600-160967000	Weak transcription	Stomach Mucosa	stomach
44	chr1:160960600-160967000	Weak transcription	GM12878-XiMat	blood
45	chr1:160960600-160967000	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr1:160960600-160967200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:160960600-160967200	Weak transcription	HepG2	liver
48	chr1:160960600-160967400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:160960600-160967600	Weak transcription	Primary T cells from cord blood	blood
50	chr1:160960600-160968000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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