Variant report

Variant	rs61978578
Chromosome Location	chr16:30408961-30408962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30408779-30412460	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30407328..30409721-chr16:30430312..30432675,2	MCF-7	breast:
2	chr16:30386182..30395144-chr16:30402818..30414477,44	MCF-7	breast:
3	chr16:30385968..30392864-chr16:30403786..30414800,30	MCF-7	breast:
4	chr16:30387676..30396507-chr16:30404234..30411930,28	K562	blood:
5	chr16:30407687..30410209-chr16:30656586..30658459,2	MCF-7	breast:
6	chr16:30401749..30403997-chr16:30408377..30410909,4	K562	blood:
7	chr16:30378819..30383918-chr16:30407597..30413128,8	MCF-7	breast:
8	chr16:30368801..30385970-chr16:30403825..30413311,30	MCF-7	breast:
9	chr16:30061476..30064810-chr16:30408529..30411930,3	MCF-7	breast:
10	chr16:30384243..30394929-chr16:30405602..30409736,14	K562	blood:

No data

Variant related genes	Relation type
SEPT1	TF binding region
ENSG00000180209	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000199787	Chromatin interaction
ENSG00000169221	Chromatin interaction
ENSG00000149925	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000270466	Chromatin interaction
ENSG00000149926	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12919022	0.90[ASN][1000 genomes]
rs12929884	0.88[ASN][1000 genomes]
rs5013201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62056262	0.88[ASN][1000 genomes]
rs71389462	0.83[AMR][1000 genomes]
rs71389465	0.83[AMR][1000 genomes]
rs7404540	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv905725	chr16:30376959-30420851	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv962197	chr16:30390489-30425618	Enhancers Weak transcription Strong transcription Active TSS Flanking 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	37 gene(s)	inside rSNPs	diseases
9	nsv1782	chr16:30391812-30410266	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61978578	ENSG00000180035	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30407600-30409200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr16:30407600-30409200	Weak transcription	Aorta	Aorta
3	chr16:30407600-30411000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:30407600-30411400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr16:30407800-30409000	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr16:30407800-30409000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr16:30407800-30409000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr16:30407800-30409000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr16:30407800-30409200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr16:30407800-30409200	Weak transcription	Adipose Nuclei	Adipose
11	chr16:30407800-30409200	Enhancers	Stomach Mucosa	stomach
12	chr16:30407800-30410800	Weak transcription	HSMM	muscle
13	chr16:30407800-30410800	Weak transcription	NHDF-Ad	bronchial
14	chr16:30407800-30411000	Weak transcription	Fetal Kidney	kidney
15	chr16:30407800-30411200	Weak transcription	Psoas Muscle	Psoas
16	chr16:30408000-30409000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr16:30408000-30409000	Genic enhancers	Fetal Thymus	thymus
18	chr16:30408000-30409000	Weak transcription	NHLF	lung
19	chr16:30408000-30409000	Weak transcription	Osteobl	bone
20	chr16:30408000-30409200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr16:30408000-30410000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr16:30408000-30410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr16:30408000-30410600	Weak transcription	NH-A	brain
24	chr16:30408000-30410800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr16:30408000-30410800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr16:30408000-30411000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr16:30408000-30411000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr16:30408000-30411000	Weak transcription	Brain Angular Gyrus	brain
29	chr16:30408000-30411000	Weak transcription	Brain Substantia Nigra	brain
30	chr16:30408000-30411000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr16:30408000-30411000	Weak transcription	Fetal Lung	lung
32	chr16:30408000-30411000	Weak transcription	Right Atrium	heart
33	chr16:30408000-30411000	Weak transcription	GM12878-XiMat	blood
34	chr16:30408000-30411200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr16:30408000-30411200	Weak transcription	HMEC	breast
36	chr16:30408200-30409000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr16:30408200-30409200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr16:30408200-30409200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr16:30408200-30410000	Genic enhancers	Dnd41	blood
40	chr16:30408200-30410200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr16:30408200-30410200	Genic enhancers	Brain Germinal Matrix	brain
42	chr16:30408200-30410800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr16:30408200-30411000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr16:30408200-30411200	Weak transcription	Small Intestine	intestine
45	chr16:30408200-30411400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr16:30408400-30409200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr16:30408400-30409400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr16:30408400-30410000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr16:30408400-30410000	Strong transcription	Brain Anterior Caudate	brain
50	chr16:30408400-30410000	Strong transcription	Fetal Muscle Trunk	muscle

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