Variant report

Variant	rs8040412
Chromosome Location	chr15:39923968-39923969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39871401..39883645-chr15:39918779..39926575,24	MCF-7	breast:
2	chr15:39901531..39904246-chr15:39922575..39924532,2	MCF-7	breast:
3	chr15:39923096..39925308-chr15:39927555..39929722,2	K562	blood:
4	chr15:39887137..39895767-chr15:39912868..39924962,20	MCF-7	breast:
5	chr15:39884252..39886366-chr15:39922051..39924260,2	MCF-7	breast:
6	chr15:39884563..39886445-chr15:39923081..39926308,3	MCF-7	breast:
7	chr15:39875425..39876319-chr15:39923488..39924115,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction
ENSG00000150667	Chromatin interaction
ENSG00000259279	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10520139	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969468	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969529	1.00[AMR][1000 genomes]
rs4468582	0.94[YRI][hapmap];0.94[AFR][1000 genomes]
rs57832843	1.00[AMR][1000 genomes]
rs7168558	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393242	1.00[AMR][1000 genomes]
rs73393273	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8028707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs937959	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	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

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39913200-39924000	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr15:39916000-39924000	Enhancers	HMEC	breast
3	chr15:39916400-39937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:39917600-39926200	Weak transcription	Esophagus	oesophagus
5	chr15:39920000-39924400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:39920200-39924400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:39920600-39924200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:39920800-39924400	Enhancers	NHEK	skin
9	chr15:39920800-39925200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:39921200-39924400	Enhancers	Fetal Heart	heart
11	chr15:39921400-39924400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:39921400-39926200	Weak transcription	Pancreas	Pancrea
13	chr15:39921400-39937600	Weak transcription	Psoas Muscle	Psoas
14	chr15:39921600-39924000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:39923000-39924000	Enhancers	HSMMtube	muscle
16	chr15:39923400-39924000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr15:39923400-39924400	Enhancers	NH-A	brain
18	chr15:39923600-39924000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:39923600-39925400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:39923800-39924000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr15:39923800-39924000	Enhancers	HSMM	muscle
22	chr15:39923800-39926200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:39923800-39939600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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