Variant report

Variant	rs1635529
Chromosome Location	chr12:48395102-48395103
allele	A/C
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	SMARCB1	chr12:48394643-48396159	Hela-S3	cervix:	n/a	n/a
2	RFX5	chr12:48394821-48395565	Hela-S3	cervix:	n/a	n/a
3	MAFK	chr12:48394799-48395336	Hela-S3	cervix:	n/a	n/a
4	MXI1	chr12:48394773-48395269	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr12:48394684-48396207	ECC-1	luminal epithelium:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948 chr12:48395771-48395781
6	MAX	chr12:48394684-48395560	Hela-S3	cervix:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
7	SMC3	chr12:48394748-48395567	Hela-S3	cervix:	n/a	n/a
8	USF2	chr12:48394767-48395244	Hela-S3	cervix:	n/a	n/a
9	MAX	chr12:48394706-48395286	MCF-7	breast:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
10	GTF2F1	chr12:48394686-48395275	Hela-S3	cervix:	n/a	n/a
11	MYC	chr12:48394758-48395121	H1-hESC	embryonic stem cell:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
12	POLR2A	chr12:48394899-48395668	SK-N-MC	brain:	n/a	n/a
13	CHD2	chr12:48394741-48395793	Hela-S3	cervix:	n/a	n/a
14	HA-E2F1	chr12:48394653-48395663	MCF-7	breast:	n/a	chr12:48395408-48395417 chr12:48395378-48395392 chr12:48395422-48395432
15	TEAD4	chr12:48394633-48395104	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr12:48395092-48395598	Hela-S3	cervix:	n/a	n/a
17	ZBTB7A	chr12:48395040-48395783	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr12:48394843-48395117	A549	lung:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
19	E2F4	chr12:48394832-48395717	MCF10A-Er-Src	breast:	n/a	chr12:48395408-48395417 chr12:48395378-48395392 chr12:48395422-48395432
20	BRCA1	chr12:48394802-48395428	Hela-S3	cervix:	n/a	n/a
21	TCF7L2	chr12:48394816-48395527	Hela-S3	cervix:	n/a	n/a
22	RAD21	chr12:48394748-48395197	Hela-S3	cervix:	n/a	chr12:48395118-48395125
23	FOS	chr12:48394872-48395113	MCF10A-Er-Src	breast:	n/a	n/a
24	MAX	chr12:48394626-48395927	HCT-116	colon:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948 chr12:48395771-48395781
25	USF2	chr12:48394771-48395114	H1-hESC	embryonic stem cell:	n/a	n/a
26	HDAC2	chr12:48394644-48396832	MCF-7	breast:	n/a	n/a
27	SIN3A	chr12:48394675-48396247	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr12:48394702-48395510	Hela-S3	cervix:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
29	ZBTB7A	chr12:48395036-48396013	ECC-1	luminal epithelium:	n/a	n/a
30	MYC	chr12:48394709-48395592	MCF10A-Er-Src	breast:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
31	MXI1	chr12:48394775-48395558	Hela-S3	cervix:	n/a	n/a
32	TCF12	chr12:48395072-48396101	ECC-1	luminal epithelium:	n/a	chr12:48395173-48395181
33	ELK1	chr12:48394794-48395264	Hela-S3	cervix:	n/a	n/a
34	MAX	chr12:48394618-48395642	A549	lung:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
35	MAX	chr12:48394662-48395179	A549	lung:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
36	MAZ	chr12:48394760-48395651	Hela-S3	cervix:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394948
37	KAP1	chr12:48394655-48397087	HEK293	kidney:	n/a	n/a
38	MAX	chr12:48394786-48395167	SK-N-SH	brain:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
39	E2F6	chr12:48394646-48395574	H1-hESC	embryonic stem cell:	n/a	chr12:48395408-48395417 chr12:48395378-48395392 chr12:48395422-48395432
40	MAX	chr12:48394611-48395738	MCF-7	breast:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
41	MAX	chr12:48394693-48395168	H1-hESC	embryonic stem cell:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
42	MYC	chr12:48394816-48395144	Hela-S3	cervix:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
43	MAX	chr12:48394684-48395425	H1-hESC	embryonic stem cell:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
44	POLR2A	chr12:48395083-48395558	Hela-S3	cervix:	n/a	n/a
45	E2F6	chr12:48394650-48395620	A549	lung:	n/a	chr12:48395408-48395417 chr12:48395378-48395392 chr12:48395422-48395432
46	MYC	chr12:48394765-48395445	MCF10A-Er-Src	breast:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
47	KAP1	chr12:48394709-48395488	U2OS	brain:	n/a	n/a
48	TBP	chr12:48394745-48395361	Hela-S3	cervix:	n/a	n/a
49	RCOR1	chr12:48394758-48395634	Hela-S3	cervix:	n/a	n/a
50	MAX	chr12:48394736-48395152	H1-hESC	embryonic stem cell:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948

No.	Distal block	Cell Line	Cell type
1	chr12:48298685..48300649-chr12:48393830..48395808,2	MCF-7	breast:
2	chr12:48297374..48299237-chr12:48393563..48396184,2	MCF-7	breast:
3	chr12:48355944..48359601-chr12:48393326..48397759,4	MCF-7	breast:
4	chr12:48394829..48397203-chr12:48403090..48404738,2	MCF-7	breast:
5	chr12:48393217..48395308-chr12:48444642..48446730,2	MCF-7	breast:
6	chr12:48360987..48363483-chr12:48393695..48396604,4	MCF-7	breast:
7	chr1:149224213..149224733-chr12:48394914..48395631,2	Hela-S3	cervix:
8	chr12:48393252..48397718-chr12:48414474..48419166,5	MCF-7	breast:
9	chr12:48393914..48396723-chr12:48402943..48405805,2	K562	blood:
10	chr12:48342574..48344961-chr12:48394535..48396923,2	MCF-7	breast:
11	chr12:48356300..48358721-chr12:48393251..48396453,4	MCF-7	breast:

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000111424	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000257955	Chromatin interaction
ENSG00000134291	Chromatin interaction
ENSG00000258203	Chromatin interaction
ENSG00000257985	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1034762	0.83[EUR][1000 genomes]
rs10783226	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783227	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11612578	0.82[EUR][1000 genomes]
rs1635526	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1635528	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635534	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1635535	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1635536	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1793912	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1793913	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1793915	0.85[AMR][1000 genomes]
rs1793917	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1793931	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1793933	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1793955	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1793956	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1859441	0.81[EUR][1000 genomes]
rs1859444	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1990029	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3803182	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3803183	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3803184	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825404	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760615	0.80[EUR][1000 genomes]
rs6580647	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580649	0.81[EUR][1000 genomes]
rs7132668	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72644841	0.82[EUR][1000 genomes]
rs7305954	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7310579	0.80[EUR][1000 genomes]
rs7957764	0.80[EUR][1000 genomes]
rs917055	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9651993	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9805048	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1635529	ZNF641	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48394200-48396000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:48394600-48395200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
3	chr12:48394600-48395200	Enhancers	Pancreas	Pancrea
4	chr12:48394600-48395200	Flanking Active TSS	Hela-S3	cervix
5	chr12:48394600-48395200	Flanking Active TSS	NHEK	skin
6	chr12:48394600-48395400	Bivalent Enhancer	Primary T cells from cord blood	blood
7	chr12:48394600-48395400	Flanking Active TSS	HMEC	breast
8	chr12:48394600-48395600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:48394600-48395800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:48394600-48396000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:48394600-48396200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr12:48394800-48395200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:48394800-48395200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:48394800-48395200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:48394800-48395200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
16	chr12:48394800-48395200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
17	chr12:48394800-48395200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:48394800-48395200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
19	chr12:48394800-48395200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
20	chr12:48394800-48395200	Bivalent/Poised TSS	Fetal Brain Female	brain
21	chr12:48394800-48395200	Flanking Active TSS	Fetal Heart	heart
22	chr12:48394800-48395200	Enhancers	Lung	lung
23	chr12:48394800-48395200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
24	chr12:48394800-48395200	Bivalent Enhancer	Stomach Mucosa	stomach
25	chr12:48394800-48395200	Flanking Bivalent TSS/Enh	A549	lung
26	chr12:48394800-48395400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr12:48394800-48395400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:48394800-48395400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
29	chr12:48394800-48395400	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:48394800-48395400	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
31	chr12:48394800-48395600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:48394800-48395800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
33	chr12:48394800-48395800	Bivalent Enhancer	Fetal Brain Male	brain
34	chr12:48394800-48395800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
35	chr12:48394800-48396000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr12:48394800-48396000	Bivalent Enhancer	Fetal Lung	lung
37	chr12:48394800-48396200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:48394800-48396400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:48394800-48396600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
40	chr12:48394800-48396600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
41	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
43	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
44	chr12:48394800-48397000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
45	chr12:48394800-48397200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr12:48394800-48397800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:48394800-48397800	Enhancers	Spleen	Spleen
48	chr12:48394800-48398600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
49	chr12:48394800-48398800	Bivalent Enhancer	Liver	Liver
50	chr12:48394800-48399200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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