Variant report

Variant	rs3753560
Chromosome Location	chr1:175162196-175162197
allele	C/G
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	CTCF	chr1:175162140-175162290	NHEK	skin:	n/a	n/a
2	CTBP2	chr1:175161323-175163077	H1-hESC	embryonic stem cell:	n/a	n/a
3	RCOR1	chr1:175160845-175162680	K562	blood:	n/a	n/a
4	YY1	chr1:175162087-175162412	K562	blood:	n/a	chr1:175162328-175162339 chr1:175162263-175162272 chr1:175162271-175162281 chr1:175162330-175162344
5	TBP	chr1:175160991-175162574	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr1:175161973-175162255	K562	blood:	n/a	n/a
7	CTCF	chr1:175161947-175162372	GM19238	blood:	n/a	chr1:175162135-175162148
8	SMARCC1	chr1:175161173-175163079	Hela-S3	cervix:	n/a	n/a
9	TBL1XR1	chr1:175161292-175162347	K562	blood:	n/a	n/a
10	IRF1	chr1:175160797-175162815	K562	blood:	n/a	chr1:175161058-175161071 chr1:175161058-175161072 chr1:175161057-175161071 chr1:175162259-175162273 chr1:175161053-175161067 chr1:175161057-175161077 chr1:175161059-175161073 chr1:175161338-175161351 chr1:175161051-175161071 chr1:175161058-175161071 chr1:175161057-175161070 chr1:175161053-175161070 chr1:175161055-175161069 chr1:175161059-175161069
11	MAX	chr1:175160954-175162593	K562	blood:	n/a	n/a
12	ZNF263	chr1:175160625-175163127	HEK293-T-REx	kidney:	n/a	chr1:175160916-175160925
13	MAX	chr1:175161860-175162438	K562	blood:	n/a	n/a
14	SP1	chr1:175161919-175162356	A549	lung:	n/a	chr1:175162261-175162273 chr1:175162262-175162271 chr1:175162262-175162276 chr1:175162262-175162271 chr1:175162263-175162272 chr1:175162261-175162273
15	CTCF	chr1:175162080-175162230	GM06990	blood:	n/a	chr1:175162135-175162148
16	ZKSCAN1	chr1:175161486-175162540	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr1:175162180-175162330	HRPEpiC	eye:	n/a	n/a
18	EGR1	chr1:175161858-175162415	K562	blood:	n/a	chr1:175161976-175161990 chr1:175162263-175162273
19	ELF1	chr1:175161957-175162548	K562	blood:	n/a	chr1:175162263-175162275
20	POLR2A	chr1:175160872-175162810	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT1	chr1:175162036-175162540	GM12878	blood:	n/a	chr1:175162373-175162382 chr1:175162441-175162452 chr1:175162443-175162452 chr1:175162442-175162451 chr1:175162372-175162381 chr1:175162409-175162420 chr1:175162259-175162271
22	YY1	chr1:175162028-175162415	ECC-1	luminal epithelium:	n/a	chr1:175162328-175162339 chr1:175162263-175162272 chr1:175162271-175162281 chr1:175162330-175162344
23	STAT1	chr1:175161083-175163061	Hela-S3	cervix:	n/a	chr1:175162373-175162382 chr1:175162441-175162452 chr1:175162443-175162452 chr1:175162442-175162451 chr1:175162372-175162381 chr1:175162409-175162420 chr1:175162259-175162271
24	POLR2A	chr1:175161364-175162580	K562	blood:	n/a	n/a
25	YY1	chr1:175161976-175162392	K562	blood:	n/a	chr1:175162328-175162339 chr1:175162263-175162272 chr1:175162271-175162281 chr1:175162330-175162344
26	E2F6	chr1:175162066-175162395	K562	blood:	n/a	chr1:175162263-175162272 chr1:175162260-175162272 chr1:175162225-175162236 chr1:175162238-175162249
27	GATA3	chr1:175161931-175162493	T-47D	breast:	n/a	n/a
28	CTCF	chr1:175161842-175162505	GM12878	blood:	n/a	chr1:175162135-175162148
29	POLR2A	chr1:175160620-175163581	MCF10A-Er-Src	breast:	n/a	n/a
30	ELF1	chr1:175161966-175162234	HepG2	liver:	n/a	n/a
31	CTCFL	chr1:175162169-175162358	K562	blood:	n/a	n/a
32	JUND	chr1:175162115-175162413	H1-hESC	embryonic stem cell:	n/a	chr1:175162264-175162273
33	YY1	chr1:175161992-175162453	ECC-1	luminal epithelium:	n/a	chr1:175162328-175162339 chr1:175162263-175162272 chr1:175162271-175162281 chr1:175162330-175162344
34	RUNX3	chr1:175161933-175162276	GM12878	blood:	n/a	n/a
35	HDAC2	chr1:175161770-175162359	MCF-7	breast:	n/a	n/a
36	POLR2A	chr1:175161587-175162491	K562	blood:	n/a	n/a
37	E2F6	chr1:175161965-175162951	H1-hESC	embryonic stem cell:	n/a	chr1:175162263-175162272 chr1:175162260-175162272 chr1:175162225-175162236 chr1:175162238-175162249
38	EGR1	chr1:175161720-175162558	HCT-116	colon:	n/a	chr1:175161976-175161990 chr1:175162263-175162273
39	POLR2A	chr1:175161747-175162558	MCF-7	breast:	n/a	n/a
40	MYC	chr1:175161995-175162921	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr1:175160461-175162587	GM18505	blood:	n/a	n/a
42	ZNF143	chr1:175161976-175162472	K562	blood:	n/a	n/a
43	TAF1	chr1:175161666-175162467	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr1:175161596-175162532	SK-N-MC	brain:	n/a	n/a
45	YY1	chr1:175161868-175162393	GM12891	blood:	n/a	chr1:175162328-175162339 chr1:175162263-175162272 chr1:175162271-175162281 chr1:175162330-175162344
46	POLR2A	chr1:175161562-175162273	GM12878	blood:	n/a	n/a
47	MAX	chr1:175161809-175162396	A549	lung:	n/a	n/a
48	POLR2A	chr1:175161678-175162493	GM10847	blood:	n/a	n/a
49	CTCF	chr1:175162160-175162310	HRE	kidney:	n/a	n/a
50	TEAD4	chr1:175161931-175162694	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:175162153-175162203	HMEC	breast:	n/a
2	chr1:175162153-175162203	NH-A	brain:	n/a
3	chr1:175162153-175162203	HCT-116	colon:	n/a
4	chr1:175162153-175162203	SAEC	small airway:	n/a
5	chr1:175162153-175162203	HRCEpiC	kidney:	n/a
6	chr1:175162153-175162203	HUVEC	blood vessel:	n/a
7	chr1:175162153-175162203	HCM	heart:	n/a
8	chr1:175162153-175162203	HAEpiC	amniotic membrane:	n/a
9	chr1:175162153-175162203	NT2-D1	testis:	n/a
10	chr1:175162153-175162203	NB4	blood:	n/a
11	chr1:175162153-175162203	HRE	kidney:	n/a
12	chr1:175162153-175162203	GM19239	blood:	n/a
13	chr1:175162153-175162203	Hepatocyte	liver:	n/a
14	chr1:175162153-175162203	HPAEpiC	pulmonary alveolar:	n/a
15	chr1:175162153-175162203	BJ	skin:	n/a
16	chr1:175162153-175162203	H1-hESC	embryonic stem cell:	embryo
17	chr1:175162153-175162203	HIPEpiC	eye:	n/a
18	chr1:175162153-175162203	GM12892	blood:	n/a
19	chr1:175162153-175162203	HL-60	blood:	n/a
20	chr1:175162153-175162203	AG04449	skin:	fetal
21	chr1:175162153-175162203	HEK293	kidney:	embryo
22	chr1:175162153-175162203	GM06990	blood:	n/a
23	chr1:175162153-175162203	NHBE	bronchial:	n/a
24	chr1:175162153-175162203	PrEC	prostate:	n/a
25	chr1:175162153-175162203	Jurkat	blood:	n/a
26	chr1:175162153-175162203	MCF10A-Er-Src	breast:	n/a
27	chr1:175162153-175162203	ovcar-3	ovarian:	n/a
28	chr1:175162153-175162203	AG09319	gingival:	n/a
29	chr1:175162153-175162203	PFSK-1	brain:	n/a
30	chr1:175162153-175162203	Caco-2	colon:	n/a
31	chr1:175162153-175162203	MCF-7	breast:	n/a
32	chr1:175162153-175162203	K562	blood:	n/a
33	chr1:175162153-175162203	AoSMC	blood vessel:	n/a
34	chr1:175162153-175162203	HNPCEpiC	eye:	n/a
35	chr1:175162153-175162203	SKMC	muscle:	n/a
36	chr1:175162153-175162203	HEEpiC	esophagus:	n/a
37	chr1:175162153-175162203	AG10803	skin:	n/a
38	chr1:175162153-175162203	BE2_C	brain:	n/a
39	chr1:175162153-175162203	A549	lung:	n/a
40	chr1:175162153-175162203	U87	brain:	n/a
41	chr1:175162153-175162203	SK-N-SH	brain:	n/a
42	chr1:175162153-175162203	IMR90	lung:	fetal
43	chr1:175162153-175162203	NHDF-neo	bronchial:	n/a
44	chr1:175162153-175162203	PANC-1	pancreas:	n/a
45	chr1:175162153-175162203	HepG2	liver:	n/a
46	chr1:175162153-175162203	GM12878	blood:	n/a
47	chr1:175162153-175162203	T-47D	breast:	n/a
48	chr1:175162153-175162203	CMK	blood:	n/a
49	chr1:175162153-175162203	Hela-S3	cervix:	n/a
50	chr1:175162153-175162203	HCPEpiC	choroid plexus:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175160599..175162642-chr17:57913163..57915904,2	MCF-7	breast:
2	chr1:175160152..175162627-chr1:176175775..176178430,2	MCF-7	breast:

Variant related genes	Relation type
KIAA0040	TF binding region
KIAA0040	CpG island
ENSG00000236021	Chromatin interaction
ENSG00000143207	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1008459	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2205604	0.89[ASN][1000 genomes]
rs2272785	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3753559	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766686	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949473	chr1:175151666-175391741	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv15667	chr1:175161934-175163375	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3753560	KIAA0040	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175158400-175162800	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:175159200-175162600	Active TSS	Lung	lung
3	chr1:175159800-175162600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:175160400-175162200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr1:175160400-175162200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:175160400-175162200	Active TSS	GM12878-XiMat	blood
7	chr1:175160400-175162400	Active TSS	Colonic Mucosa	Colon
8	chr1:175160400-175162400	Active TSS	Pancreas	Pancrea
9	chr1:175160400-175162600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr1:175160600-175162200	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr1:175160600-175162400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:175160600-175162400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:175160600-175162400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr1:175160600-175163000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:175160600-175163200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:175160800-175162200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:175160800-175162200	Active TSS	Primary B cells from peripheral blood	blood
18	chr1:175160800-175162200	Active TSS	Primary T cells fromperipheralblood	blood
19	chr1:175160800-175162200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:175160800-175162200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr1:175160800-175162200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:175160800-175162200	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr1:175160800-175162200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:175160800-175162200	Active TSS	HMEC	breast
25	chr1:175160800-175162200	Active TSS	NHEK	skin
26	chr1:175160800-175162400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:175160800-175162400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:175160800-175162400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:175160800-175162400	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr1:175160800-175162400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr1:175160800-175162400	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr1:175160800-175162400	Active TSS	Esophagus	oesophagus
33	chr1:175160800-175162400	Active TSS	Fetal Muscle Trunk	muscle
34	chr1:175160800-175162400	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:175160800-175162400	Active TSS	Right Atrium	heart
36	chr1:175160800-175162400	Active TSS	Right Ventricle	heart
37	chr1:175160800-175162400	Active TSS	Small Intestine	intestine
38	chr1:175160800-175162600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr1:175160800-175162600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:175160800-175162600	Active TSS	Aorta	Aorta
41	chr1:175160800-175162600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:175160800-175162600	Active TSS	Fetal Kidney	kidney
43	chr1:175160800-175162600	Active TSS	Gastric	stomach
44	chr1:175160800-175162600	Active TSS	Ovary	ovary
45	chr1:175160800-175162600	Active TSS	Psoas Muscle	Psoas
46	chr1:175160800-175162800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:175160800-175162800	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr1:175160800-175163000	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr1:175161000-175162200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:175161000-175162200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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