Variant report

Variant	rs1669833
Chromosome Location	chr15:45076214-45076215
allele	C/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:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:44954130..44956261-chr15:45073217..45077809,7	K562	blood:
2	chr15:45074115..45076771-chr15:45078811..45081683,3	K562	blood:
3	chr15:44949692..44958566-chr15:45073635..45082479,18	K562	blood:
4	chr15:44970663..44972208-chr15:45073819..45076712,2	K562	blood:
5	chr15:45050487..45053149-chr15:45073962..45077607,3	K562	blood:
6	chr15:44829337..44830847-chr15:45073722..45076273,2	K562	blood:
7	chr15:45007223..45009349-chr15:45075066..45077596,2	K562	blood:
8	chr15:45068193..45071978-chr15:45073632..45077696,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PATL2-4	chr15:45075779-45076489	NONHSAT042194

No data

Variant related genes	Relation type
ENSG00000104133	Chromatin interaction
ENSG00000166710	Chromatin interaction
ENSG00000104131	Chromatin interaction
ENSG00000185880	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10163110	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1137516	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11634059	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11634063	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11639157	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12912870	1.00[EUR][1000 genomes]
rs1630168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669834	0.85[JPT][hapmap]
rs1690313	0.87[EUR][1000 genomes]
rs16974543	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869125	0.87[EUR][1000 genomes]
rs1901530	0.87[EUR][1000 genomes]
rs1901536	0.82[YRI][hapmap]
rs1901538	0.94[EUR][1000 genomes]
rs1901539	0.88[AFR][1000 genomes]
rs2167595	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2444011	0.86[AFR][1000 genomes]
rs2468067	0.94[EUR][1000 genomes]
rs2470908	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2470916	0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs2960206	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3100130	0.90[AFR][1000 genomes]
rs3100140	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3100141	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3100144	0.83[AFR][1000 genomes]
rs3110180	0.88[AFR][1000 genomes]
rs3110674	0.83[AFR][1000 genomes]
rs3110677	0.94[EUR][1000 genomes]
rs3759878	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3759881	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4625702	0.80[YRI][hapmap]
rs4923989	1.00[CEU][hapmap]
rs4923990	0.93[EUR][1000 genomes]
rs4923991	0.94[EUR][1000 genomes]
rs4923993	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs62024991	0.87[EUR][1000 genomes]
rs62025968	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62025969	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6416439	0.87[EUR][1000 genomes]
rs6416440	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6493110	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6493111	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6493114	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6493116	0.94[EUR][1000 genomes]
rs6493118	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6493119	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6493124	0.94[EUR][1000 genomes]
rs6493125	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6493126	0.94[EUR][1000 genomes]
rs6493127	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493128	0.94[EUR][1000 genomes]
rs7151	0.87[EUR][1000 genomes]
rs7168090	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7172357	0.94[EUR][1000 genomes]
rs7172376	0.94[EUR][1000 genomes]
rs7496437	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7496559	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8035787	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs8036223	0.87[EUR][1000 genomes]
rs8038532	0.97[EUR][1000 genomes]
rs935885	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs935888	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs935889	1.00[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking 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 target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	nsv819242	chr15:45059351-45078608	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
6	nsv457123	chr15:45074519-45099142	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
7	nsv569302	chr15:45074519-45099142	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45075200-45076400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:45075200-45076400	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:45075400-45076400	Weak transcription	HSMM	muscle
4	chr15:45075400-45076400	Weak transcription	HSMMtube	muscle
5	chr15:45075600-45077000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr15:45075800-45076400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:45075800-45077200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr15:45076000-45076400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:45076000-45076400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr15:45076000-45076400	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr15:45076000-45076400	Flanking Active TSS	GM12878-XiMat	blood
12	chr15:45076000-45076400	Flanking Active TSS	HMEC	breast
13	chr15:45076000-45076400	Flanking Active TSS	K562	blood
14	chr15:45076000-45076400	Flanking Active TSS	NH-A	brain
15	chr15:45076000-45076600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:45076000-45076600	Enhancers	Small Intestine	intestine
17	chr15:45076000-45077000	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr15:45076000-45077000	Active TSS	Brain Cingulate Gyrus	brain
19	chr15:45076000-45077000	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr15:45076000-45077000	Active TSS	Colon Smooth Muscle	Colon
21	chr15:45076000-45077200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:45076000-45077200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:45076000-45077200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:45076000-45077200	Active TSS	Brain Anterior Caudate	brain
25	chr15:45076000-45077200	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr15:45076200-45076400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr15:45076200-45076400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:45076200-45076400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr15:45076200-45076400	Active TSS	Primary B cells from cord blood	blood
30	chr15:45076200-45076400	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr15:45076200-45076400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr15:45076200-45076400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr15:45076200-45076400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr15:45076200-45076400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr15:45076200-45076400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr15:45076200-45076400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:45076200-45076400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr15:45076200-45076400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:45076200-45076400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:45076200-45076400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:45076200-45076400	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr15:45076200-45076400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:45076200-45076400	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr15:45076200-45076400	Enhancers	Fetal Intestine Small	intestine
45	chr15:45076200-45076400	Enhancers	Fetal Kidney	kidney
46	chr15:45076200-45076400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr15:45076200-45076400	Flanking Active TSS	Hela-S3	cervix
48	chr15:45076200-45076400	Flanking Active TSS	NHLF	lung
49	chr15:45076200-45076600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr15:45076200-45076600	Flanking Active TSS	Primary B cells from peripheral blood	blood

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