Variant report

Variant	rs40446
Chromosome Location	chr16:75496658-75496659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr16:75496548-75496942	HepG2	liver:	n/a	chr16:75496714-75496729
2	FOXA1	chr16:75496435-75496975	HepG2	liver:	n/a	chr16:75496714-75496729

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75495533..75500726-chr16:75509549..75515784,9	MCF-7	breast:
2	chr16:75465991..75469604-chr16:75494524..75499996,12	MCF-7	breast:
3	chr16:75496396..75498894-chr16:75652662..75656672,3	MCF-7	breast:
4	chr16:75492503..75494041-chr16:75496484..75498203,2	K562	blood:
5	chr16:75475154..75477431-chr16:75495274..75497923,2	MCF-7	breast:
6	chr16:75492483..75495341-chr16:75495841..75499470,4	K562	blood:
7	chr16:75495991..75500241-chr16:75679416..75683319,6	MCF-7	breast:
8	chr16:75496436..75498553-chr16:75596400..75601675,4	MCF-7	breast:
9	chr16:75496580..75498737-chr16:75588829..75590831,2	MCF-7	breast:
10	chr16:75465942..75469515-chr16:75494275..75497182,4	K562	blood:
11	chr16:75464062..75469543-chr16:75495268..75500189,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261476	TF binding region
ENSG00000065427	Chromatin interaction
ENSG00000205084	Chromatin interaction
ENSG00000153774	Chromatin interaction
ENSG00000166848	Chromatin interaction
ENSG00000034713	Chromatin interaction
ENSG00000065457	Chromatin interaction
ENSG00000261476	Chromatin interaction
ENSG00000203472	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs100912	0.86[ASN][1000 genomes]
rs1030261	0.97[ASN][1000 genomes]
rs1030262	0.98[ASN][1000 genomes]
rs10871311	0.80[ASN][1000 genomes]
rs10871312	0.97[ASN][1000 genomes]
rs10871313	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11149831	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11641249	0.96[ASN][1000 genomes]
rs11641430	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11641801	0.80[ASN][1000 genomes]
rs11643207	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11644306	0.97[ASN][1000 genomes]
rs11644639	0.80[ASN][1000 genomes]
rs11648176	0.80[ASN][1000 genomes]
rs11649638	0.97[ASN][1000 genomes]
rs11865296	0.83[ASN][1000 genomes]
rs12051137	0.95[ASN][1000 genomes]
rs12149063	0.80[ASN][1000 genomes]
rs12444589	0.80[ASN][1000 genomes]
rs12446877	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12448829	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12918797	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12924333	0.94[ASN][1000 genomes]
rs12927562	0.96[ASN][1000 genomes]
rs12928036	0.96[ASN][1000 genomes]
rs12929673	0.81[ASN][1000 genomes]
rs12932606	0.85[ASN][1000 genomes]
rs12933281	0.96[ASN][1000 genomes]
rs1424013	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542864	0.81[ASN][1000 genomes]
rs166013	0.84[EUR][1000 genomes]
rs17696831	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834013	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834014	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161684	0.94[ASN][1000 genomes]
rs247454	0.88[ASN][1000 genomes]
rs2738809	0.88[ASN][1000 genomes]
rs2738812	0.82[ASN][1000 genomes]
rs2738813	0.82[ASN][1000 genomes]
rs2738814	0.83[ASN][1000 genomes]
rs28558946	0.97[ASN][1000 genomes]
rs2865528	0.80[ASN][1000 genomes]
rs28655617	0.95[ASN][1000 genomes]
rs3115960	0.90[ASN][1000 genomes]
rs34021527	0.85[ASN][1000 genomes]
rs34539062	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34918083	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34996006	0.93[ASN][1000 genomes]
rs35209155	0.81[ASN][1000 genomes]
rs35214308	0.93[ASN][1000 genomes]
rs35683383	0.94[ASN][1000 genomes]
rs37592	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37593	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37594	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37595	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37597	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs37599	0.82[ASN][1000 genomes]
rs37602	0.82[ASN][1000 genomes]
rs37605	0.81[ASN][1000 genomes]
rs37606	0.96[ASN][1000 genomes]
rs4887825	0.81[ASN][1000 genomes]
rs4887829	0.97[ASN][1000 genomes]
rs4888415	0.80[ASN][1000 genomes]
rs4888425	0.93[ASN][1000 genomes]
rs4888426	0.93[ASN][1000 genomes]
rs4888427	0.94[ASN][1000 genomes]
rs4888430	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888431	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4888432	0.87[ASN][1000 genomes]
rs56004344	0.86[ASN][1000 genomes]
rs56116092	0.94[ASN][1000 genomes]
rs59155720	0.94[ASN][1000 genomes]
rs59347518	0.92[ASN][1000 genomes]
rs59465235	0.96[ASN][1000 genomes]
rs62060550	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62060551	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564261	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188604	0.80[ASN][1000 genomes]
rs7191890	0.83[ASN][1000 genomes]
rs7193828	0.89[ASN][1000 genomes]
rs7194035	0.89[ASN][1000 genomes]
rs7195161	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198873	0.92[ASN][1000 genomes]
rs7199062	0.93[ASN][1000 genomes]
rs7199132	0.80[ASN][1000 genomes]
rs7200053	0.93[ASN][1000 genomes]
rs7202596	0.97[ASN][1000 genomes]
rs7204984	0.93[ASN][1000 genomes]
rs7206665	0.93[ASN][1000 genomes]
rs8055490	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8055974	0.81[ASN][1000 genomes]
rs8056141	0.83[ASN][1000 genomes]
rs8057084	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8063068	0.96[ASN][1000 genomes]
rs977985	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs977986	0.81[ASN][1000 genomes]
rs977987	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9923834	0.81[ASN][1000 genomes]
rs9933255	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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	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
2	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
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	esv2758432	chr16:75419614-75576971	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	esv2758657	chr16:75419614-75576971	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv457521	chr16:75487758-75603925	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv572979	chr16:75487758-75603925	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs40446	CFDP1	Cis_1M	lymphoblastoid	RTeQTL
rs40446	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs40446	RP11-252K23.2	cis	Thyroid	GTEx
rs40446	RP11-252K23.2	cis	lung	GTEx
rs40446	RP11-252K23.2	cis	Skin Sun Exposed Lower leg	GTEx
rs40446	RP11-252K23.2	cis	Artery Tibial	GTEx
rs40446	RP11-252K23.2	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75468800-75497000	Weak transcription	NHLF	lung
2	chr16:75469400-75497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:75469400-75497400	Weak transcription	Psoas Muscle	Psoas
4	chr16:75477800-75497000	Weak transcription	NHDF-Ad	bronchial
5	chr16:75481800-75497600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr16:75484000-75496800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:75485400-75496800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr16:75485600-75497200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr16:75485800-75496800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr16:75485800-75496800	Weak transcription	Fetal Kidney	kidney
11	chr16:75485800-75496800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr16:75485800-75497000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr16:75485800-75497000	Weak transcription	Fetal Thymus	thymus
14	chr16:75485800-75497000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr16:75485800-75497200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr16:75485800-75497400	Weak transcription	Fetal Brain Female	brain
17	chr16:75485800-75497600	Weak transcription	Aorta	Aorta
18	chr16:75486000-75496800	Weak transcription	Thymus	Thymus
19	chr16:75486400-75496800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr16:75489000-75496800	Weak transcription	K562	blood
21	chr16:75489800-75497400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr16:75491000-75496800	Enhancers	Fetal Intestine Large	intestine
23	chr16:75491800-75497200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr16:75491800-75497200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr16:75491800-75497400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr16:75492000-75496800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr16:75492600-75497000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr16:75492600-75497400	Weak transcription	Pancreas	Pancrea
29	chr16:75493000-75497400	Enhancers	Primary T cells fromperipheralblood	blood
30	chr16:75493200-75497000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr16:75493200-75497000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr16:75493800-75496800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr16:75493800-75497000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr16:75493800-75497000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr16:75493800-75497000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr16:75493800-75497000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr16:75494000-75497000	Weak transcription	Right Atrium	heart
38	chr16:75494000-75497400	Weak transcription	Gastric	stomach
39	chr16:75494200-75496800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr16:75494200-75497000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr16:75494200-75497200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr16:75494400-75497000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr16:75494400-75497000	Weak transcription	HSMMtube	muscle
44	chr16:75494400-75497200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr16:75494400-75497400	Enhancers	Fetal Lung	lung
46	chr16:75494600-75496800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr16:75494600-75497000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr16:75494600-75497000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:75494600-75497000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr16:75494600-75497000	Enhancers	Hela-S3	cervix

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