Variant report

Variant	rs1635528
Chromosome Location	chr12:48395900-48395901
allele	A/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	SMARCB1	chr12:48394643-48396159	Hela-S3	cervix:	n/a	n/a
2	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
3	FOXA1	chr12:48395710-48396125	T-47D	breast:	n/a	n/a
4	POLR2A	chr12:48395173-48395988	H1-neurons	neurons:	n/a	n/a
5	NRF1	chr12:48395126-48395997	SK-N-SH	brain:	n/a	chr12:48395407-48395421
6	FOXA2	chr12:48395684-48396160	A549	lung:	n/a	n/a
7	GATA3	chr12:48395754-48396385	T-47D	breast:	n/a	n/a
8	MAX	chr12:48395778-48397117	MCF-7	breast:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
9	FOXA1	chr12:48395730-48396198	HepG2	liver:	n/a	n/a
10	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
11	HDAC2	chr12:48394644-48396832	MCF-7	breast:	n/a	n/a
12	SIN3A	chr12:48394675-48396247	H1-hESC	embryonic stem cell:	n/a	n/a
13	FOXA2	chr12:48395732-48396143	A549	lung:	n/a	n/a
14	ZBTB7A	chr12:48395036-48396013	ECC-1	luminal epithelium:	n/a	n/a
15	FOXA1	chr12:48395813-48396162	HepG2	liver:	n/a	n/a
16	FOXA1	chr12:48395782-48396134	T-47D	breast:	n/a	n/a
17	TCF12	chr12:48395072-48396101	ECC-1	luminal epithelium:	n/a	chr12:48395173-48395181
18	FOXA2	chr12:48395789-48396125	HepG2	liver:	n/a	n/a
19	KAP1	chr12:48394655-48397087	HEK293	kidney:	n/a	n/a
20	MAX	chr12:48395799-48397245	A549	lung:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
21	EP300	chr12:48395773-48396254	T-47D	breast:	n/a	chr12:48395971-48395981
22	YY1	chr12:48395448-48396269	H1-hESC	embryonic stem cell:	n/a	chr12:48395774-48395785 chr12:48396070-48396079 chr12:48395773-48395782 chr12:48396098-48396114
23	MXI1	chr12:48394606-48397189	SK-N-SH	brain:	n/a	n/a
24	TCF7L2	chr12:48395864-48396189	PANC-1	pancreas:	n/a	n/a
25	ZNF263	chr12:48394775-48396398	HEK293-T-REx	kidney:	n/a	chr12:48396283-48396292
26	GATA3	chr12:48395750-48396205	T-47D	breast:	n/a	n/a
27	MAX	chr12:48394712-48397112	ECC-1	luminal epithelium:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48396876-48396883 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48396875-48396884 chr12:48394939-48394948 chr12:48395771-48395781 chr12:48396872-48396887
28	CTBP2	chr12:48394745-48396786	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:48395868-48395918	NHBE	bronchial:	n/a
2	chr12:48395868-48395918	HCM	heart:	n/a
3	chr12:48395868-48395918	HPAEpiC	pulmonary alveolar:	n/a
4	chr12:48395868-48395918	H1-hESC	embryonic stem cell:	embryo
5	chr12:48395868-48395918	AG09319	gingival:	n/a
6	chr12:48395868-48395918	HIPEpiC	eye:	n/a
7	chr12:48395868-48395918	IMR90	lung:	fetal
8	chr12:48395868-48395918	HUVEC	blood vessel:	n/a
9	chr12:48395868-48395918	CMK	blood:	n/a
10	chr12:48395868-48395918	AG04449	skin:	fetal
11	chr12:48395868-48395918	SKMC	muscle:	n/a
12	chr12:48395868-48395918	K562	blood:	n/a
13	chr12:48395868-48395918	HEK293	kidney:	embryo
14	chr12:48395868-48395918	HCF	heart:	n/a
15	chr12:48395868-48395918	HNPCEpiC	eye:	n/a
16	chr12:48395868-48395918	ProgFib	skin:	n/a
17	chr12:48395868-48395918	LNCaP	prostate:	n/a
18	chr12:48395868-48395918	GM19239	blood:	n/a
19	chr12:48395868-48395918	NHDF-neo	bronchial:	n/a
20	chr12:48395868-48395918	PFSK-1	brain:	n/a
21	chr12:48395868-48395918	HCPEpiC	choroid plexus:	n/a
22	chr12:48395868-48395918	Jurkat	blood:	n/a
23	chr12:48395868-48395918	NB4	blood:	n/a
24	chr12:48395868-48395918	HL-60	blood:	n/a
25	chr12:48395868-48395918	HEEpiC	esophagus:	n/a
26	chr12:48395868-48395918	AG04450	lung:	fetal
27	chr12:48395868-48395918	PANC-1	pancreas:	n/a
28	chr12:48395868-48395918	Caco-2	colon:	n/a
29	chr12:48395868-48395918	AoSMC	blood vessel:	n/a
30	chr12:48395868-48395918	HAEpiC	amniotic membrane:	n/a
31	chr12:48395868-48395918	SK-N-SH	brain:	n/a
32	chr12:48395868-48395918	U87	brain:	n/a
33	chr12:48395868-48395918	AG09309	skin:	n/a
34	chr12:48395868-48395918	RPTEC	kidney:	n/a
35	chr12:48395868-48395918	NT2-D1	testis:	n/a
36	chr12:48395868-48395918	T-47D	breast:	n/a
37	chr12:48395868-48395918	ECC-1	luminal epithelium:	n/a
38	chr12:48395868-48395918	HepG2	liver:	n/a
39	chr12:48395868-48395918	HCT-116	colon:	n/a
40	chr12:48395868-48395918	A549	lung:	n/a
41	chr12:48395868-48395918	HRE	kidney:	n/a
42	chr12:48395868-48395918	ovcar-3	ovarian:	n/a
43	chr12:48395868-48395918	HRCEpiC	kidney:	n/a
44	chr12:48395868-48395918	MCF10A-Er-Src	breast:	n/a
45	chr12:48395868-48395918	PrEC	prostate:	n/a
46	chr12:48395868-48395918	MCF-7	breast:	n/a
47	chr12:48395868-48395918	HMEC	breast:	n/a
48	chr12:48395868-48395918	Hepatocyte	liver:	n/a
49	chr12:48395868-48395918	SK-N-SH_RA	brain:	n/a
50	chr12:48395868-48395918	SAEC	small airway:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48297374..48299237-chr12:48393563..48396184,2	MCF-7	breast:
2	chr12:48355944..48359601-chr12:48393326..48397759,4	MCF-7	breast:
3	chr12:48394829..48397203-chr12:48403090..48404738,2	MCF-7	breast:
4	chr12:48360987..48363483-chr12:48393695..48396604,4	MCF-7	breast:
5	chr12:48393252..48397718-chr12:48414474..48419166,5	MCF-7	breast:
6	chr12:48393914..48396723-chr12:48402943..48405805,2	K562	blood:
7	chr12:48342574..48344961-chr12:48394535..48396923,2	MCF-7	breast:
8	chr12:48356300..48358721-chr12:48393251..48396453,4	MCF-7	breast:

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

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10783226	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10783227	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635526	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635529	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635534	0.84[AMR][1000 genomes]
rs1635535	0.84[AMR][1000 genomes]
rs1635536	0.81[AMR][1000 genomes]
rs1793912	0.84[AMR][1000 genomes]
rs1793913	0.84[AMR][1000 genomes]
rs1793915	0.83[AMR][1000 genomes]
rs1793917	0.84[AMR][1000 genomes]
rs1793931	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793933	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793955	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793956	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1859444	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1990029	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3803182	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3803183	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803184	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825404	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580647	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7132668	0.81[ASN][1000 genomes]
rs7305954	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs917055	0.84[AMR][1000 genomes]
rs9651993	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9805048	0.81[AMR][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
rs1635528	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:124 , 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	chr12:48394600-48396000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr12:48394600-48396200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr12:48394800-48396000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr12:48394800-48396000	Bivalent Enhancer	Fetal Lung	lung
6	chr12:48394800-48396200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:48394800-48396400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:48394800-48396600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
9	chr12:48394800-48396600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
10	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
12	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
13	chr12:48394800-48397000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
14	chr12:48394800-48397200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
15	chr12:48394800-48397800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:48394800-48397800	Enhancers	Spleen	Spleen
17	chr12:48394800-48398600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
18	chr12:48394800-48398800	Bivalent Enhancer	Liver	Liver
19	chr12:48394800-48399200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:48395000-48396000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr12:48395000-48396000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:48395000-48396000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr12:48395000-48396000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr12:48395000-48396200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:48395000-48396200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:48395000-48396200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
27	chr12:48395000-48396200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
28	chr12:48395000-48396400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:48395000-48396400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
30	chr12:48395000-48396400	Active TSS	HSMMtube	muscle
31	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
34	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
35	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
36	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Osteobl	bone
37	chr12:48395000-48396800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr12:48395000-48396800	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
41	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
43	chr12:48395000-48397000	Active TSS	Aorta	Aorta
44	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
45	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
46	chr12:48395000-48398000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:48395000-48398800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
48	chr12:48395000-48399200	Bivalent Enhancer	Fetal Thymus	thymus
49	chr12:48395200-48396000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:48395200-48396000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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