Variant report

Variant	rs999675
Chromosome Location	chr16:75306402-75306403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr16:75306184-75306530	GM12878	blood:	n/a	chr16:75306216-75306230
2	CTCF	chr16:75306300-75306450	GM12868	blood:	n/a	n/a
3	YY1	chr16:75306146-75306618	HepG2	liver:	n/a	chr16:75306216-75306230
4	RUNX3	chr16:75306164-75306470	GM12878	blood:	n/a	n/a
5	MAZ	chr16:75306288-75306450	HepG2	liver:	n/a	n/a
6	RUNX3	chr16:75305862-75306496	GM12878	blood:	n/a	n/a
7	EBF1	chr16:75305841-75306458	GM12878	blood:	n/a	chr16:75306052-75306063
8	EBF1	chr16:75305709-75306452	GM12878	blood:	n/a	chr16:75306052-75306063
9	SPI1	chr16:75306204-75306478	GM12878	blood:	n/a	chr16:75306337-75306350
10	YY1	chr16:75306174-75306569	GM12892	blood:	n/a	chr16:75306216-75306230
11	MAZ	chr16:75306298-75306472	GM12878	blood:	n/a	n/a
12	MTA3	chr16:75305803-75306499	GM12878	blood:	n/a	n/a
13	MYC	chr16:75306215-75306415	NB4	blood:	n/a	n/a
14	SPI1	chr16:75306187-75306484	GM12891	blood:	n/a	chr16:75306337-75306350
15	CTCF	chr16:75306280-75306430	GM12867	blood:	n/a	n/a
16	CTCF	chr16:75306360-75306510	GM12864	blood:	n/a	n/a
17	POLR2A	chr16:75306273-75306636	HL-60	blood:	n/a	n/a
18	SPI1	chr16:75306128-75306490	HL-60	blood:	n/a	chr16:75306337-75306350

No.	Distal block	Cell Line	Cell type
1	chr16:75305715..75307833-chr16:75412001..75414049,2	MCF-7	breast:
2	chr16:75305411..75308006-chr16:75310161..75314701,4	MCF-7	breast:
3	chr14:32394037..32396201-chr16:75304956..75307730,2	MCF-7	breast:
4	chr16:75306196..75308145-chr16:75363526..75365550,2	MCF-7	breast:
5	chr16:75299873..75302816-chr16:75305752..75307580,2	K562	blood:
6	chr16:75284875..75286553-chr16:75305358..75307613,2	K562	blood:

Variant related genes	Relation type
BCAR1	TF binding region
ENSG00000050820	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1001861	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781976	0.88[CHD][hapmap]
rs1109342	0.83[CHD][hapmap]
rs11149831	0.83[CEU][hapmap]
rs11640018	0.86[CHD][hapmap]
rs12444589	0.83[CHD][hapmap]
rs12919951	0.94[ASN][1000 genomes]
rs12928974	0.99[ASN][1000 genomes]
rs1559339	0.83[CHD][hapmap]
rs166013	0.83[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs17696696	0.83[CHD][hapmap]
rs2865826	0.99[ASN][1000 genomes]
rs2865827	0.97[ASN][1000 genomes]
rs35263058	0.83[CHD][hapmap]
rs4243111	0.86[CHD][hapmap]
rs4638613	0.83[CHD][hapmap]
rs4888368	0.86[ASN][1000 genomes]
rs4888378	0.83[CHD][hapmap]
rs4888380	0.83[CHD][hapmap]
rs4993969	0.83[CHD][hapmap]
rs7195324	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs766521	0.83[CHD][hapmap]
rs8046109	0.81[CHD][hapmap]
rs8050059	0.83[CHD][hapmap]
rs999674	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv516504	chr16:75223491-75306402	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	esv1806781	chr16:75235390-75307470	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv906909	chr16:75236154-75316074	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv906910	chr16:75251299-75316074	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv906912	chr16:75252526-75320827	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
12	nsv906913	chr16:75267743-75306402	Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
13	nsv471095	chr16:75269533-75320827	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
14	nsv833283	chr16:75302175-75392308	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs999675	RP11-252K23.2	cis	Thyroid	GTEx
rs999675	RP11-252K23.2	cis	Artery Tibial	GTEx
rs999675	RP11-252K23.2	cis	Skin Sun Exposed Lower leg	GTEx
rs999675	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs999675	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75301000-75325000	Weak transcription	Liver	Liver
2	chr16:75301800-75321800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr16:75302000-75315800	Weak transcription	Fetal Brain Female	brain
4	chr16:75302000-75324000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr16:75302200-75307400	Weak transcription	Osteobl	bone
6	chr16:75302400-75306800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:75302400-75306800	Weak transcription	HMEC	breast
8	chr16:75302400-75307000	Weak transcription	NHEK	skin
9	chr16:75302400-75307200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:75302400-75307200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr16:75302400-75307400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr16:75302400-75313400	Weak transcription	HSMM	muscle
13	chr16:75302400-75314600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr16:75302600-75313400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr16:75303800-75306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr16:75304400-75307600	Enhancers	Placenta	Placenta
17	chr16:75305000-75307200	Enhancers	Fetal Muscle Leg	muscle
18	chr16:75305400-75307800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr16:75305400-75307800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr16:75305400-75309000	Enhancers	GM12878-XiMat	blood
21	chr16:75305600-75306600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr16:75305600-75307000	Enhancers	Fetal Stomach	stomach
23	chr16:75305600-75307200	Enhancers	Fetal Heart	heart
24	chr16:75305600-75307800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr16:75305600-75307800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr16:75305600-75307800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr16:75305600-75307800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr16:75305600-75307800	Enhancers	NHLF	lung
29	chr16:75305800-75306600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr16:75305800-75306600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr16:75305800-75307000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr16:75305800-75307200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
33	chr16:75305800-75307200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr16:75305800-75307600	Enhancers	Lung	lung
35	chr16:75305800-75307600	Enhancers	Spleen	Spleen
36	chr16:75305800-75307800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr16:75305800-75307800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr16:75305800-75308000	Enhancers	HUVEC	blood vessel
39	chr16:75306000-75306600	Enhancers	Primary hematopoietic stem cells	blood
40	chr16:75306000-75306600	Enhancers	Hela-S3	cervix
41	chr16:75306000-75306600	Enhancers	HSMMtube	muscle
42	chr16:75306000-75307000	Weak transcription	NHDF-Ad	bronchial
43	chr16:75306000-75313200	Weak transcription	Left Ventricle	heart
44	chr16:75306000-75313400	Weak transcription	Pancreas	Pancrea
45	chr16:75306200-75306600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr16:75306200-75306600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr16:75306200-75306600	Weak transcription	A549	lung
48	chr16:75306200-75306800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr16:75306200-75325000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr16:75306200-75325200	Weak transcription	H1 Cell Line	embryonic stem cell

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