Variant report

Variant	rs568652
Chromosome Location	chr15:40389870-40389871
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40342956..40345791-chr15:40389827..40392011,2	MCF-7	breast:
2	chr15:40379925..40381610-chr15:40389500..40391529,2	MCF-7	breast:
3	chr15:40361459..40366979-chr15:40389781..40395512,5	MCF-7	breast:
4	chr15:40388598..40390113-chr15:40390447..40392056,2	K562	blood:
5	chr15:40389103..40392679-chr15:40452401..40455332,4	K562	blood:
6	chr15:39872166..39874631-chr15:40388813..40390537,2	MCF-7	breast:
7	chr15:40389070..40391081-chr15:40419316..40421072,2	K562	blood:
8	chr15:40328740..40331785-chr15:40389787..40392261,3	K562	blood:
9	chr15:40357794..40362220-chr15:40389488..40392528,3	MCF-7	breast:
10	chr15:40372039..40375867-chr15:40386826..40392262,4	K562	blood:
11	chr15:40336782..40338579-chr15:40387773..40390430,2	MCF-7	breast:
12	chr15:40388597..40390833-chr15:40440085..40442294,2	K562	blood:
13	chr15:40384830..40387803-chr15:40388131..40391380,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259409	Chromatin interaction
ENSG00000140319	Chromatin interaction
ENSG00000137801	Chromatin interaction
ENSG00000248508	Chromatin interaction
ENSG00000156970	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11631335	0.89[EUR][1000 genomes]
rs12592048	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs495654	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs500804	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs511338	0.82[AFR][1000 genomes]
rs537455	0.83[CEU][hapmap]
rs543399	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs569539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675173	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs770470	0.95[AMR][1000 genomes];0.99[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	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
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40381000-40390200	Genic enhancers	Fetal Stomach	stomach
2	chr15:40381800-40390200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:40383400-40394000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr15:40383600-40390400	Genic enhancers	Fetal Thymus	thymus
5	chr15:40383600-40390800	Genic enhancers	Fetal Intestine Small	intestine
6	chr15:40384000-40390600	Enhancers	Primary B cells from cord blood	blood
7	chr15:40384200-40390000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:40384200-40392400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:40385000-40390600	Weak transcription	Fetal Brain Female	brain
10	chr15:40385200-40390400	Enhancers	Primary T cells from cord blood	blood
11	chr15:40385400-40390000	Weak transcription	Osteobl	bone
12	chr15:40385400-40390200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:40385600-40390000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:40385600-40390200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr15:40385600-40390600	Weak transcription	Fetal Brain Male	brain
16	chr15:40385800-40390000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:40385800-40390000	Enhancers	Stomach Smooth Muscle	stomach
18	chr15:40385800-40390200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:40386000-40390000	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr15:40386000-40390400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:40386000-40390600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:40386200-40390000	Enhancers	HepG2	liver
23	chr15:40386600-40390400	Genic enhancers	Thymus	Thymus
24	chr15:40386800-40390000	Weak transcription	Esophagus	oesophagus
25	chr15:40386800-40390200	Enhancers	Rectal Smooth Muscle	rectum
26	chr15:40387200-40390000	Enhancers	K562	blood
27	chr15:40387200-40392800	Enhancers	Fetal Intestine Large	intestine
28	chr15:40387200-40395600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:40387200-40397800	Enhancers	Fetal Muscle Leg	muscle
30	chr15:40387400-40390200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:40387400-40390800	Enhancers	Primary B cells from peripheral blood	blood
32	chr15:40387400-40395200	Enhancers	NHLF	lung
33	chr15:40387600-40390400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:40387600-40390400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr15:40387600-40391400	Enhancers	Psoas Muscle	Psoas
36	chr15:40387600-40395200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:40387600-40397200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr15:40387800-40390600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr15:40387800-40390800	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:40387800-40391000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:40388000-40390000	Enhancers	Colon Smooth Muscle	Colon
42	chr15:40388000-40390400	Enhancers	NHDF-Ad	bronchial
43	chr15:40388000-40390600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr15:40388000-40390600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:40388000-40390600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:40388000-40391000	Flanking Active TSS	GM12878-XiMat	blood
47	chr15:40388000-40393800	Enhancers	Fetal Kidney	kidney
48	chr15:40388200-40390000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:40388200-40390000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:40388200-40390000	Enhancers	Pancreatic Islets	Pancreatic Islet

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