Variant report

Variant	rs675173
Chromosome Location	chr15:40394859-40394860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40376791..40380091-chr15:40393802..40397569,3	MCF-7	breast:
2	chr15:40361459..40366979-chr15:40389781..40395512,5	MCF-7	breast:
3	chr15:40343717..40348357-chr15:40394391..40397717,7	MCF-7	breast:
4	chr15:40345188..40347486-chr15:40391657..40395509,4	MCF-7	breast:
5	chr15:40339870..40341521-chr15:40394237..40395838,2	MCF-7	breast:
6	chr15:40328572..40331875-chr15:40394053..40397065,4	MCF-7	breast:
7	chr15:40329348..40332922-chr15:40394377..40398986,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248508	Chromatin interaction
ENSG00000140319	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11631335	0.91[EUR][1000 genomes]
rs12592048	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs495654	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537455	0.84[CEU][hapmap]
rs543399	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs568652	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]
rs569539	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	0.99[AMR][1000 genomes];0.98[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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40387200-40395600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr15:40387200-40397800	Enhancers	Fetal Muscle Leg	muscle
3	chr15:40387400-40395200	Enhancers	NHLF	lung
4	chr15:40387600-40395200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:40387600-40397200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr15:40389200-40400000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:40389800-40400400	Enhancers	Small Intestine	intestine
8	chr15:40390400-40399800	Transcr. at gene 5' and 3'	Thymus	Thymus
9	chr15:40391000-40395000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:40391000-40395000	Enhancers	Adipose Nuclei	Adipose
11	chr15:40391000-40399800	Enhancers	Liver	Liver
12	chr15:40391200-40395200	Enhancers	Duodenum Mucosa	Duodenum
13	chr15:40391200-40398800	Enhancers	Placenta	Placenta
14	chr15:40391400-40395000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr15:40391400-40395000	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr15:40391400-40395000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr15:40391400-40395200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr15:40391400-40395400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:40391400-40395400	Enhancers	HSMM	muscle
20	chr15:40391400-40396600	Genic enhancers	Fetal Thymus	thymus
21	chr15:40391400-40396800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr15:40391400-40397600	Enhancers	NH-A	brain
23	chr15:40391400-40400000	Enhancers	Stomach Mucosa	stomach
24	chr15:40391600-40395000	Enhancers	Primary hematopoietic stem cells	blood
25	chr15:40391600-40395200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:40391600-40395200	Enhancers	Rectal Smooth Muscle	rectum
27	chr15:40392000-40400000	Enhancers	Right Atrium	heart
28	chr15:40392000-40400000	Enhancers	Right Ventricle	heart
29	chr15:40392000-40400400	Enhancers	Pancreas	Pancrea
30	chr15:40392200-40400200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr15:40392400-40395200	Genic enhancers	Fetal Stomach	stomach
32	chr15:40392400-40395200	Genic enhancers	HSMMtube	muscle
33	chr15:40392400-40395400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:40392400-40395400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
35	chr15:40392400-40395800	Genic enhancers	Fetal Intestine Small	intestine
36	chr15:40392400-40397200	Genic enhancers	Primary B cells from peripheral blood	blood
37	chr15:40392400-40397600	Enhancers	Psoas Muscle	Psoas
38	chr15:40392400-40398400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:40392600-40395000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:40392600-40395400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:40392600-40396600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:40392600-40398600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:40392800-40395200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:40392800-40397800	Enhancers	Lung	lung
45	chr15:40393000-40395200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr15:40393000-40395200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:40393200-40395000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:40393200-40395000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:40393400-40395000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:40393400-40395000	Enhancers	NHDF-Ad	bronchial

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