Variant report

Variant	rs620407
Chromosome Location	chr15:40081435-40081436
allele	A/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40080851..40082524-chr15:40092879..40095618,2	MCF-7	breast:
2	chr15:39960830..39961348-chr15:40081129..40081640,2	MCF-7	breast:
3	chr15:40081008..40084255-chr15:40089544..40091959,3	MCF-7	breast:
4	chr15:40080889..40083832-chr15:40212318..40214554,2	K562	blood:
5	chr15:39960376..39961266-chr15:40081056..40081843,2	MCF-7	breast:
6	chr15:40081168..40081951-chr15:40166868..40167816,2	K562	blood:
7	chr15:40074604..40078535-chr15:40078976..40081815,4	K562	blood:
8	chr15:40080053..40082265-chr15:40095277..40098030,2	K562	blood:
9	chr15:40074241..40077863-chr15:40078792..40081577,3	K562	blood:
10	chr15:40077135..40079271-chr15:40079393..40081898,2	MCF-7	breast:
11	chr15:40080849..40083373-chr15:40085760..40088536,2	K562	blood:
12	chr15:40079722..40082305-chr15:40603620..40606001,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261136	Chromatin interaction
ENSG00000166073	Chromatin interaction
ENSG00000244705	Chromatin interaction
ENSG00000259580	Chromatin interaction
ENSG00000246863	Chromatin interaction
ENSG00000150667	Chromatin interaction
ENSG00000259198	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10520153	0.89[CEU][hapmap]
rs1166718	0.84[ASN][1000 genomes]
rs1166722	0.86[ASN][1000 genomes]
rs1166723	0.82[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs12592687	0.81[ASN][1000 genomes]
rs1688087	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2576929	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2576932	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2576933	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2631714	0.83[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs2638009	0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs34943556	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4115216	0.83[JPT][hapmap]
rs4924389	0.82[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs4924391	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs592172	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs594863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606927	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6492915	0.96[JPT][hapmap]
rs6492919	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66496275	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs670748	0.84[ASN][1000 genomes]
rs7165244	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7179417	0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs8033957	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40076000-40103200	Weak transcription	Right Atrium	heart
2	chr15:40076600-40081600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:40076600-40082000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:40076600-40082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:40076600-40082600	Weak transcription	Primary T cells from cord blood	blood
6	chr15:40076600-40084200	Weak transcription	Adipose Nuclei	Adipose
7	chr15:40076600-40086200	Weak transcription	Fetal Muscle Leg	muscle
8	chr15:40076600-40090200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:40076600-40092600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:40076800-40082200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr15:40076800-40082400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:40077200-40082600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:40077200-40082600	Enhancers	NHLF	lung
14	chr15:40077200-40092600	Weak transcription	NHEK	skin
15	chr15:40077200-40093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:40077400-40082600	Enhancers	Osteobl	bone
17	chr15:40077600-40082400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr15:40077600-40094600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:40077800-40082600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr15:40078000-40082000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr15:40078200-40082400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr15:40078600-40081600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:40078600-40082400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:40078600-40082400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:40078800-40082000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:40078800-40082600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr15:40078800-40082600	Enhancers	NHDF-Ad	bronchial
28	chr15:40079000-40082800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:40079400-40082200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr15:40079600-40082600	Enhancers	Fetal Lung	lung
31	chr15:40080000-40095600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:40080200-40084400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:40080400-40084800	Weak transcription	HUVEC	blood vessel
34	chr15:40080400-40095000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr15:40080600-40082000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:40080600-40085800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:40081000-40082000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr15:40081000-40092400	Weak transcription	HSMMtube	muscle
39	chr15:40081200-40082000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:40081200-40082600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:40081200-40084400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:40081200-40085200	Weak transcription	K562	blood
43	chr15:40081200-40089600	Weak transcription	HSMM	muscle
44	chr15:40081200-40090400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:40081200-40092200	Weak transcription	NH-A	brain
46	chr15:40081200-40093400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:40081400-40081600	Enhancers	Fetal Kidney	kidney
48	chr15:40081400-40088600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:40081400-40092800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:40081400-40100200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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