Variant report

Variant	rs247450
Chromosome Location	chr16:75490017-75490018
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75482835..75485909-chr16:75488077..75491215,3	MCF-7	breast:
2	chr16:75488552..75490455-chr16:75493804..75496037,3	MCF-7	breast:
3	chr16:75486898..75488534-chr16:75489987..75492131,2	K562	blood:
4	chr16:75488273..75491906-chr16:75496881..75500144,3	K562	blood:
5	chr16:75489832..75492687-chr16:75493360..75496513,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261717	Chromatin interaction
ENSG00000261476	Chromatin interaction
ENSG00000166822	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1030261	0.81[ASN][1000 genomes]
rs1030262	0.81[ASN][1000 genomes]
rs1074961	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10871312	0.81[ASN][1000 genomes]
rs11644306	0.82[ASN][1000 genomes]
rs11645691	0.81[ASN][1000 genomes]
rs11646418	0.82[EUR][1000 genomes]
rs11649638	0.81[ASN][1000 genomes]
rs12446903	0.82[ASN][1000 genomes]
rs12927562	0.81[ASN][1000 genomes]
rs12928036	0.81[ASN][1000 genomes]
rs12932952	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12933281	0.81[ASN][1000 genomes]
rs12935329	0.80[ASN][1000 genomes]
rs1540	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs185052	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs185053	0.90[ASN][1000 genomes]
rs2059257	0.85[EUR][1000 genomes]
rs2242405	0.99[ASN][1000 genomes]
rs247423	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247424	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247425	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247427	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247431	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247434	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247436	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247437	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs247438	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247443	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247447	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28558946	0.81[ASN][1000 genomes]
rs2865527	0.82[ASN][1000 genomes]
rs28655617	0.80[ASN][1000 genomes]
rs37588	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs37589	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs37596	0.94[ASN][1000 genomes]
rs37599	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37601	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs37602	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37605	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3844219	0.83[EUR][1000 genomes]
rs3851735	0.83[EUR][1000 genomes]
rs3851736	0.85[EUR][1000 genomes]
rs40217	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs42472	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs455407	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs467223	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs467780	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs468079	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4887827	0.91[ASN][1000 genomes]
rs4887828	0.99[ASN][1000 genomes]
rs4887829	0.81[ASN][1000 genomes]
rs4887830	0.87[ASN][1000 genomes]
rs4888393	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4888394	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4888395	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4888396	0.82[ASN][1000 genomes]
rs4888398	0.82[ASN][1000 genomes]
rs4993971	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59465235	0.81[ASN][1000 genomes]
rs62062595	0.93[EUR][1000 genomes]
rs6564256	0.85[EUR][1000 genomes]
rs7201989	0.83[ASN][1000 genomes]
rs7202284	0.84[EUR][1000 genomes]
rs7202596	0.82[ASN][1000 genomes]
rs766522	0.82[ASN][1000 genomes]
rs8046184	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8046416	0.98[ASN][1000 genomes]
rs8046949	0.82[ASN][1000 genomes]
rs8048677	0.82[EUR][1000 genomes]
rs8048816	0.82[ASN][1000 genomes]
rs8049611	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8051611	0.85[EUR][1000 genomes]
rs8053632	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8054586	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8055609	0.87[EUR][1000 genomes]
rs977986	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9923834	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9928232	0.93[ASN][1000 genomes]
rs9934007	0.80[ASN][1000 genomes]
rs9989421	0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs247450	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75468800-75493800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr16:75468800-75497000	Weak transcription	NHLF	lung
3	chr16:75469400-75491000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr16:75469400-75497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr16:75469400-75497400	Weak transcription	Psoas Muscle	Psoas
6	chr16:75473600-75496000	Weak transcription	HMEC	breast
7	chr16:75477400-75494400	Weak transcription	NH-A	brain
8	chr16:75477800-75497000	Weak transcription	NHDF-Ad	bronchial
9	chr16:75479400-75493800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr16:75481800-75497600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr16:75482400-75494200	Weak transcription	GM12878-XiMat	blood
12	chr16:75483200-75495800	Weak transcription	Fetal Brain Male	brain
13	chr16:75483600-75494200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr16:75483800-75496000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr16:75484000-75490800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr16:75484000-75496600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr16:75484000-75496800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr16:75485000-75494400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr16:75485200-75493200	Weak transcription	Esophagus	oesophagus
20	chr16:75485400-75493200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr16:75485400-75496800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr16:75485600-75491000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr16:75485600-75491000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr16:75485600-75491200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr16:75485600-75493800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr16:75485600-75494200	Weak transcription	Brain Germinal Matrix	brain
27	chr16:75485600-75495800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr16:75485600-75496400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr16:75485600-75497200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr16:75485800-75490800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr16:75485800-75491600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr16:75485800-75492000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr16:75485800-75492000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr16:75485800-75493000	Weak transcription	NHEK	skin
35	chr16:75485800-75493200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr16:75485800-75493200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr16:75485800-75493600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr16:75485800-75493800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr16:75485800-75493800	Weak transcription	A549	lung
40	chr16:75485800-75493800	Weak transcription	HSMM	muscle
41	chr16:75485800-75493800	Weak transcription	HSMMtube	muscle
42	chr16:75485800-75494200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr16:75485800-75494200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr16:75485800-75494400	Weak transcription	Primary T cells from cord blood	blood
45	chr16:75485800-75494400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr16:75485800-75494600	Weak transcription	Brain Substantia Nigra	brain
47	chr16:75485800-75494600	Weak transcription	Hela-S3	cervix
48	chr16:75485800-75495200	Weak transcription	Dnd41	blood
49	chr16:75485800-75496000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr16:75485800-75496400	Weak transcription	Primary B cells from cord blood	blood

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