Variant report

Variant	rs13008809
Chromosome Location	chr2:47499792-47499793
allele	G/T
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:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47406999..47409780-chr2:47499066..47501901,2	MCF-7	breast:
2	chr2:47213912..47214423-chr2:47498901..47499882,2	MCF-7	breast:
3	chr2:47394184..47396929-chr2:47499010..47501713,3	MCF-7	breast:
4	chr2:47498345..47500843-chr2:47537583..47540511,2	MCF-7	breast:
5	chr2:47394132..47407926-chr2:47492481..47507054,74	K562	blood:
6	chr2:47442736..47444439-chr2:47498242..47500143,2	MCF-7	breast:
7	chr2:47416956..47422470-chr2:47490735..47503252,22	MCF-7	breast:
8	chr2:47397474..47405591-chr2:47490090..47505751,58	MCF-7	breast:
9	chr2:47412361..47428396-chr2:47486545..47501626,43	MCF-7	breast:
10	chr2:47213916..47214788-chr2:47499094..47500691,5	MCF-7	breast:
11	chr2:47396241..47406824-chr2:47488149..47503058,74	K562	blood:
12	chr2:47476493..47480049-chr2:47496667..47500826,6	MCF-7	breast:
13	chr2:47422552..47429870-chr2:47496148..47502457,12	MCF-7	breast:
14	chr2:47403102..47404509-chr2:47499208..47500165,9	MCF-7	breast:
15	chr2:47493422..47496136-chr2:47498839..47501811,3	MCF-7	breast:
16	chr2:47463258..47464786-chr2:47499792..47501339,2	MCF-7	breast:
17	chr2:47496586..47498213-chr2:47499758..47501672,2	MCF-7	breast:
18	chr2:47214133..47214774-chr2:47499196..47500160,4	K562	blood:
19	chr2:47497455..47500389-chr2:47501805..47505272,3	MCF-7	breast:
20	chr2:47397785..47406895-chr2:47495364..47504312,55	MCF-7	breast:
21	chr2:47497085..47500611-chr2:47536768..47542000,5	MCF-7	breast:
22	chr2:47499653..47503286-chr2:47546650..47549919,4	MCF-7	breast:
23	chr2:47403492..47404421-chr2:47499307..47500012,2	MCF-7	breast:
24	chr2:47411666..47413985-chr2:47498950..47500848,2	MCF-7	breast:
25	chr2:47477055..47479211-chr2:47498989..47500882,2	MCF-7	breast:
26	chr2:47499316..47499837-chr9:130565445..130566065,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction
ENSG00000136877	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10172988	0.81[JPT][hapmap]
rs10186190	0.85[JPT][hapmap]
rs11680357	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11894871	0.95[CEU][hapmap]
rs1391178	0.83[YRI][hapmap]
rs1553061	0.90[JPT][hapmap]
rs1979774	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6755555	0.81[JPT][hapmap]
rs7568590	0.85[CEU][hapmap]
rs904161	0.95[CEU][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9309144	0.83[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47493400-47500400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:47496000-47502200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:47497000-47501800	Weak transcription	HSMMtube	muscle
4	chr2:47498600-47500200	Active TSS	Rectal Smooth Muscle	rectum
5	chr2:47498600-47500200	Enhancers	Small Intestine	intestine
6	chr2:47498600-47500400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
7	chr2:47498600-47500600	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr2:47498800-47500000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:47498800-47500200	Flanking Active TSS	A549	lung
10	chr2:47499000-47499800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:47499000-47500400	Flanking Active TSS	HepG2	liver
12	chr2:47499000-47500600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:47499000-47502000	Enhancers	Spleen	Spleen
14	chr2:47499200-47499800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
15	chr2:47499200-47499800	Active TSS	Liver	Liver
16	chr2:47499200-47499800	Active TSS	Brain Anterior Caudate	brain
17	chr2:47499200-47499800	Active TSS	NHEK	skin
18	chr2:47499200-47500000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:47499200-47500000	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr2:47499200-47500000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr2:47499200-47500000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr2:47499200-47500000	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr2:47499200-47500000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:47499200-47500000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:47499200-47500000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:47499200-47500000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:47499200-47500000	Enhancers	Fetal Brain Male	brain
28	chr2:47499200-47500000	Flanking Active TSS	Fetal Muscle Trunk	muscle
29	chr2:47499200-47500000	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr2:47499200-47500000	Flanking Active TSS	HUVEC	blood vessel
31	chr2:47499200-47500200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:47499200-47500200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:47499200-47500200	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr2:47499200-47500200	Flanking Active TSS	Fetal Stomach	stomach
35	chr2:47499200-47500200	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr2:47499200-47500400	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr2:47499200-47500400	Flanking Active TSS	GM12878-XiMat	blood
38	chr2:47499200-47500400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr2:47499200-47500600	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr2:47499200-47500600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr2:47499200-47500800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:47499200-47502200	Enhancers	Fetal Heart	heart
43	chr2:47499200-47502200	Enhancers	NHLF	lung
44	chr2:47499400-47499800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:47499400-47499800	Active TSS	H9 Cell Line	embryonic stem cell
46	chr2:47499400-47499800	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr2:47499400-47499800	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr2:47499400-47499800	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr2:47499400-47499800	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr2:47499400-47499800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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