Variant report

Variant	rs11579939
Chromosome Location	chr1:161279518-161279519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161278785..161280602-chr1:161282077..161284441,2	MCF-7	breast:
2	chr1:161150561..161152446-chr1:161277325..161279650,2	K562	blood:
3	chr1:160989097..160992016-chr1:161278410..161280382,2	K562	blood:

Variant related genes	Relation type
ENSG00000143252	Chromatin interaction
ENSG00000158769	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11577663	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578160	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580931	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583870	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584714	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585941	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16832786	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16832847	0.85[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16832849	0.85[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832911	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832913	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832945	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4272646	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656296	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427589	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678315	1.00[CHB][hapmap]
rs6684273	1.00[YRI][hapmap]
rs72714971	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72714973	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714981	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714982	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714983	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72714985	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715002	0.92[AMR][1000 genomes]
rs7519821	1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7538701	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793329	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11579939	E2F5	trans	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161276000-161279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:161276000-161283800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:161276200-161283200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:161276200-161283600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:161276400-161279600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:161276400-161282200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:161276400-161283400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:161276400-161283400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:161276400-161283400	Weak transcription	Liver	Liver
10	chr1:161276400-161283600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:161276600-161281200	Weak transcription	Fetal Kidney	kidney
12	chr1:161276600-161282800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:161276600-161283400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:161276600-161283400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:161276600-161283400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:161276600-161283400	Weak transcription	Right Atrium	heart
17	chr1:161276600-161283600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:161276800-161283400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:161276800-161283400	Weak transcription	Brain Angular Gyrus	brain
20	chr1:161276800-161283400	Weak transcription	Brain Anterior Caudate	brain
21	chr1:161277000-161281000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:161277000-161283600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:161277200-161280200	Weak transcription	NHEK	skin
24	chr1:161277200-161283000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:161277200-161283400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:161277200-161283400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:161277200-161283400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:161277200-161283400	Weak transcription	Esophagus	oesophagus
29	chr1:161277200-161283400	Weak transcription	Pancreas	Pancrea
30	chr1:161277200-161283400	Weak transcription	Spleen	Spleen
31	chr1:161277200-161283600	Weak transcription	Left Ventricle	heart
32	chr1:161277400-161281600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:161277400-161282400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:161277400-161283200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:161277400-161283200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:161277400-161283400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:161277400-161283400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:161277400-161283400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:161278000-161279800	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr1:161278200-161279600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:161278200-161281000	Weak transcription	A549	lung
42	chr1:161278200-161283200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:161278200-161283200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:161278200-161283400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:161278200-161283400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:161278400-161279600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:161278400-161283000	Weak transcription	Dnd41	blood
48	chr1:161278400-161283200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:161278400-161283200	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr1:161278400-161283400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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