Variant report

Variant	rs247424
Chromosome Location	chr16:75458632-75458633
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75456561..75460930-chr16:75465550..75468879,6	K562	blood:
2	chr16:75457127..75459090-chr16:75459202..75462146,2	MCF-7	breast:
3	chr16:75457350..75460465-chr16:75464646..75467985,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1017239	0.88[ASN][1000 genomes]
rs1074961	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10781977	0.83[ASN][1000 genomes]
rs10871307	0.84[ASN][1000 genomes]
rs10871308	0.86[ASN][1000 genomes]
rs11149812	0.84[ASN][1000 genomes]
rs11149813	0.83[ASN][1000 genomes]
rs11149814	0.83[ASN][1000 genomes]
rs11149816	0.87[ASN][1000 genomes]
rs11641801	0.81[ASN][1000 genomes]
rs11642572	0.80[ASN][1000 genomes]
rs11644639	0.81[ASN][1000 genomes]
rs11645691	0.93[ASN][1000 genomes]
rs11646418	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11648176	0.81[ASN][1000 genomes]
rs12444589	0.81[ASN][1000 genomes]
rs12445188	0.85[ASN][1000 genomes]
rs12445211	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12445813	0.85[ASN][1000 genomes]
rs12446903	0.94[ASN][1000 genomes]
rs12449177	0.83[ASN][1000 genomes]
rs12922897	0.84[ASN][1000 genomes]
rs12932952	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12935329	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1540	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs185052	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1862705	0.86[ASN][1000 genomes]
rs1895489	0.81[ASN][1000 genomes]
rs2032926	0.88[ASN][1000 genomes]
rs2059257	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242405	0.82[ASN][1000 genomes]
rs247423	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247425	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247427	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247431	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247434	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247436	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247437	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247438	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247439	0.82[AMR][1000 genomes]
rs247443	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs247447	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs247450	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2865527	0.99[ASN][1000 genomes]
rs2865528	0.81[ASN][1000 genomes]
rs2865532	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3743606	0.80[ASN][1000 genomes]
rs37588	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs37589	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs37599	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs37601	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs37602	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs37605	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3784936	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3784937	0.86[ASN][1000 genomes]
rs3844219	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851735	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851736	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851739	0.81[ASN][1000 genomes]
rs40217	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs42472	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4536500	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs455407	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs467223	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs467780	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs468079	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4887813	0.81[ASN][1000 genomes]
rs4887814	0.83[ASN][1000 genomes]
rs4887828	0.82[ASN][1000 genomes]
rs4888374	0.84[ASN][1000 genomes]
rs4888375	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4888381	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4888393	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4888394	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4888395	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4888396	0.94[ASN][1000 genomes]
rs4888397	0.92[ASN][1000 genomes]
rs4888398	0.94[ASN][1000 genomes]
rs4993971	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62062595	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6564249	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6564256	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7192155	0.88[ASN][1000 genomes]
rs7199680	0.84[ASN][1000 genomes]
rs7201989	0.81[ASN][1000 genomes]
rs7202284	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs766522	0.94[ASN][1000 genomes]
rs8046184	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8046416	0.80[ASN][1000 genomes]
rs8046949	0.94[ASN][1000 genomes]
rs8048677	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8048816	0.94[ASN][1000 genomes]
rs8049611	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8050662	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8051611	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8051785	0.86[ASN][1000 genomes]
rs8053632	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8054586	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8055609	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs889446	0.86[ASN][1000 genomes]
rs977986	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9923834	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9933956	0.89[ASN][1000 genomes]
rs9934007	0.92[ASN][1000 genomes]
rs9989421	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1062023	chr16:75427013-75461626	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs247424	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75427200-75464400	Weak transcription	Esophagus	oesophagus
2	chr16:75427200-75465400	Weak transcription	Spleen	Spleen
3	chr16:75432400-75465400	Weak transcription	Pancreas	Pancrea
4	chr16:75432400-75466600	Weak transcription	Aorta	Aorta
5	chr16:75444000-75464400	Weak transcription	Hela-S3	cervix
6	chr16:75445200-75465000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr16:75446200-75465200	Weak transcription	Lung	lung
8	chr16:75446600-75464600	Weak transcription	Brain Germinal Matrix	brain
9	chr16:75446600-75465400	Weak transcription	Small Intestine	intestine
10	chr16:75446600-75466400	Weak transcription	Brain Angular Gyrus	brain
11	chr16:75446600-75466400	Weak transcription	Right Ventricle	heart
12	chr16:75446800-75466000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr16:75446800-75466400	Weak transcription	Fetal Brain Female	brain
14	chr16:75446800-75466400	Weak transcription	HSMM	muscle
15	chr16:75447000-75466400	Weak transcription	Liver	Liver
16	chr16:75450800-75465000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr16:75453600-75466400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr16:75453800-75466400	Weak transcription	Psoas Muscle	Psoas
19	chr16:75453800-75466600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:75455200-75460200	Weak transcription	NHLF	lung
21	chr16:75455200-75463800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr16:75455200-75465000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr16:75455200-75465400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr16:75455200-75465400	Weak transcription	Right Atrium	heart
25	chr16:75455200-75466000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr16:75455400-75460400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr16:75455400-75465400	Weak transcription	Fetal Thymus	thymus
28	chr16:75455600-75460200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr16:75455600-75465000	Weak transcription	Primary T cells from cord blood	blood
30	chr16:75455600-75465000	Weak transcription	Brain Hippocampus Middle	brain
31	chr16:75455600-75466400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr16:75455600-75466400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr16:75455600-75466400	Weak transcription	Primary B cells from cord blood	blood
34	chr16:75455600-75466400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr16:75455600-75466400	Weak transcription	NH-A	brain
36	chr16:75455800-75460200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr16:75455800-75460200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr16:75455800-75460200	Weak transcription	NHDF-Ad	bronchial
39	chr16:75455800-75460400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr16:75455800-75461200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr16:75455800-75461200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr16:75455800-75461600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr16:75455800-75462800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr16:75455800-75463800	Weak transcription	Dnd41	blood
45	chr16:75455800-75464200	Weak transcription	Fetal Stomach	stomach
46	chr16:75455800-75464400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr16:75455800-75464400	Weak transcription	Fetal Muscle Leg	muscle
48	chr16:75455800-75464600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr16:75455800-75464800	Weak transcription	GM12878-XiMat	blood
50	chr16:75455800-75465000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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