Variant report

Variant	rs61999991
Chromosome Location	chr15:33375639-33375640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:33374615..33377190-chr15:33380884..33382943,2	MCF-7	breast:
2	chr15:33359723..33362601-chr15:33373724..33376683,3	MCF-7	breast:
3	chr15:33356120..33364271-chr15:33368982..33380679,29	MCF-7	breast:
4	chr15:33359743..33360823-chr15:33375465..33376496,5	MCF-7	breast:
5	chr15:33368885..33371162-chr15:33373678..33376639,3	MCF-7	breast:
6	chr15:33359743..33360658-chr15:33375465..33376496,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16963396	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61999985	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61999990	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61999991	ARL6IP6	trans	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33361200-33378800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:33362000-33376000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:33370400-33379200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:33370800-33377600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:33372600-33384200	Weak transcription	Brain Angular Gyrus	brain
6	chr15:33373400-33378800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:33374400-33376800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:33374400-33377200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr15:33374600-33377400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr15:33374800-33376800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:33375000-33376600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr15:33375200-33375800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:33375200-33376000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr15:33375200-33376000	Enhancers	H9 Cell Line	embryonic stem cell
15	chr15:33375200-33376000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr15:33375200-33377200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:33375200-33377200	Enhancers	HMEC	breast
18	chr15:33375200-33377200	Enhancers	NHEK	skin
19	chr15:33375400-33376600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:33375400-33380000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:33375600-33375800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr15:33375600-33375800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr15:33375600-33375800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:33375600-33376000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr15:33375600-33376000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr15:33375600-33376000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:33375600-33376000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr15:33375600-33376200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:33375600-33376200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr15:33375600-33376200	Enhancers	Esophagus	oesophagus
31	chr15:33375600-33376400	Enhancers	NHLF	lung
32	chr15:33375600-33376600	Enhancers	HSMM	muscle
33	chr15:33375600-33376800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:33375600-33376800	Enhancers	NH-A	brain
35	chr15:33375600-33377200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:33375600-33377200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr15:33375600-33377400	Enhancers	Placenta	Placenta
38	chr15:33375600-33377400	Enhancers	HSMMtube	muscle

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