Variant report

Variant	rs1540
Chromosome Location	chr16:75481185-75481186
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75479224..75481746-chr16:75483426..75485775,2	MCF-7	breast:
2	chr16:75480575..75482180-chr16:75497109..75499874,2	K562	blood:
3	chr16:75466529..75469115-chr16:75481185..75484731,5	MCF-7	breast:
4	chr16:75474256..75476578-chr16:75479632..75482029,2	MCF-7	breast:
5	chr16:75467452..75469743-chr16:75480979..75483108,3	K562	blood:
6	chr16:75480575..75485333-chr16:75494576..75499874,6	K562	blood:

Variant related genes	Relation type
ENSG00000261717	Chromatin interaction
ENSG00000153774	Chromatin interaction
ENSG00000166822	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1017239	0.80[ASN][1000 genomes]
rs1030261	0.81[ASN][1000 genomes]
rs1030262	0.80[ASN][1000 genomes]
rs1074961	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10871312	0.81[ASN][1000 genomes]
rs11644306	0.81[ASN][1000 genomes]
rs11645691	0.82[ASN][1000 genomes]
rs11646418	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11649638	0.81[ASN][1000 genomes]
rs12446903	0.84[ASN][1000 genomes]
rs12927562	0.82[ASN][1000 genomes]
rs12928036	0.82[ASN][1000 genomes]
rs12932952	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12933281	0.82[ASN][1000 genomes]
rs12935329	0.82[ASN][1000 genomes]
rs185052	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs185053	0.89[ASN][1000 genomes]
rs2032926	0.80[ASN][1000 genomes]
rs2059257	0.86[EUR][1000 genomes]
rs2161684	0.81[ASN][1000 genomes]
rs2242405	1.00[ASN][1000 genomes]
rs247423	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs247424	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247425	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs247427	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs247431	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs247434	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs247436	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs247437	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247438	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs247443	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs247447	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247450	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28558946	0.81[ASN][1000 genomes]
rs2865527	0.83[ASN][1000 genomes]
rs35683383	0.81[ASN][1000 genomes]
rs37588	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs37589	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs37596	0.93[ASN][1000 genomes]
rs37599	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs37601	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs37602	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs37605	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3844219	0.84[EUR][1000 genomes]
rs3851735	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3851736	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs40217	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42472	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs455407	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs467223	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs467780	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs468079	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4887827	0.92[ASN][1000 genomes]
rs4887828	0.99[ASN][1000 genomes]
rs4887829	0.81[ASN][1000 genomes]
rs4887830	0.87[ASN][1000 genomes]
rs4888381	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4888393	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4888394	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4888395	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4888396	0.84[ASN][1000 genomes]
rs4888397	0.81[ASN][1000 genomes]
rs4888398	0.84[ASN][1000 genomes]
rs4888427	0.81[ASN][1000 genomes]
rs4993971	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59155720	0.81[ASN][1000 genomes]
rs59465235	0.82[ASN][1000 genomes]
rs62062595	0.96[EUR][1000 genomes]
rs6564249	0.81[EUR][1000 genomes]
rs6564256	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7201989	0.85[ASN][1000 genomes]
rs7202284	0.85[EUR][1000 genomes]
rs7202596	0.81[ASN][1000 genomes]
rs766522	0.84[ASN][1000 genomes]
rs8046184	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8046416	0.98[ASN][1000 genomes]
rs8046949	0.84[ASN][1000 genomes]
rs8048677	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8048816	0.84[ASN][1000 genomes]
rs8049611	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8050662	0.80[ASN][1000 genomes]
rs8051611	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8053632	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8054586	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8055609	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs977986	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9923834	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9928232	0.93[ASN][1000 genomes]
rs9933956	0.81[ASN][1000 genomes]
rs9934007	0.82[ASN][1000 genomes]
rs9989421	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv521596	chr16:75466696-75486648	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1540	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75468400-75482400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:75468400-75482600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:75468400-75489400	Weak transcription	Small Intestine	intestine
4	chr16:75468600-75481600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr16:75468600-75482400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr16:75468600-75487800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr16:75468600-75489800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr16:75468800-75481400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr16:75468800-75483000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr16:75468800-75483200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr16:75468800-75483600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr16:75468800-75483600	Weak transcription	Adipose Nuclei	Adipose
13	chr16:75468800-75483600	Weak transcription	Hela-S3	cervix
14	chr16:75468800-75483800	Weak transcription	HSMMtube	muscle
15	chr16:75468800-75484200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr16:75468800-75484400	Weak transcription	Brain Anterior Caudate	brain
17	chr16:75468800-75484400	Weak transcription	NHEK	skin
18	chr16:75468800-75484600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr16:75468800-75484600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr16:75468800-75484600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr16:75468800-75484800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr16:75468800-75484800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr16:75468800-75485400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr16:75468800-75486400	Weak transcription	Pancreas	Pancrea
25	chr16:75468800-75486400	Weak transcription	Right Atrium	heart
26	chr16:75468800-75486600	Weak transcription	HUVEC	blood vessel
27	chr16:75468800-75489200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr16:75468800-75493800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr16:75468800-75497000	Weak transcription	NHLF	lung
30	chr16:75469000-75483000	Weak transcription	Primary B cells from cord blood	blood
31	chr16:75469000-75483200	Weak transcription	Osteobl	bone
32	chr16:75469200-75481800	Weak transcription	A549	lung
33	chr16:75469400-75483400	Weak transcription	Fetal Brain Female	brain
34	chr16:75469400-75483600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr16:75469400-75484600	Weak transcription	Spleen	Spleen
36	chr16:75469400-75484800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr16:75469400-75484800	Weak transcription	Brain Angular Gyrus	brain
38	chr16:75469400-75484800	Weak transcription	Brain Hippocampus Middle	brain
39	chr16:75469400-75486600	Weak transcription	K562	blood
40	chr16:75469400-75491000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr16:75469400-75497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr16:75469400-75497400	Weak transcription	Psoas Muscle	Psoas
43	chr16:75470000-75482000	Weak transcription	Fetal Muscle Leg	muscle
44	chr16:75470000-75484600	Weak transcription	Right Ventricle	heart
45	chr16:75473600-75496000	Weak transcription	HMEC	breast
46	chr16:75474800-75483400	Weak transcription	Placenta	Placenta
47	chr16:75475000-75483200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr16:75475400-75481400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr16:75475800-75481400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr16:75476400-75481400	Weak transcription	Fetal Lung	lung

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