Variant report

Variant	rs1635527
Chromosome Location	chr12:48396364-48396365
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:48395754-48396385	T-47D	breast:	n/a	n/a
2	SUZ12	chr12:48396098-48398262	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr12:48395778-48397117	MCF-7	breast:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
4	HA-E2F1	chr12:48395990-48397009	MCF-7	breast:	n/a	n/a
5	NRF1	chr12:48396003-48397082	SK-N-SH	brain:	n/a	n/a
6	HDAC2	chr12:48394644-48396832	MCF-7	breast:	n/a	n/a
7	KAP1	chr12:48394655-48397087	HEK293	kidney:	n/a	n/a
8	TCF12	chr12:48396360-48397034	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr12:48395799-48397245	A549	lung:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
10	KAP1	chr12:48396036-48397040	U2OS	brain:	n/a	n/a
11	TCF7L2	chr12:48396127-48396866	HEK293	kidney:	n/a	n/a
12	MXI1	chr12:48394606-48397189	SK-N-SH	brain:	n/a	n/a
13	MAX	chr12:48396319-48397210	ECC-1	luminal epithelium:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
14	ZNF263	chr12:48394775-48396398	HEK293-T-REx	kidney:	n/a	chr12:48396283-48396292
15	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
16	CTBP2	chr12:48394745-48396786	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:48396354-48396404	AG04450	lung:	fetal
2	chr12:48396354-48396404	MCF10A-Er-Src	breast:	n/a
3	chr12:48396354-48396404	ECC-1	luminal epithelium:	n/a
4	chr12:48396354-48396404	PrEC	prostate:	n/a
5	chr12:48396354-48396404	Hela-S3	cervix:	n/a
6	chr12:48396354-48396404	U87	brain:	n/a
7	chr12:48396354-48396404	HL-60	blood:	n/a
8	chr12:48396354-48396404	HEEpiC	esophagus:	n/a
9	chr12:48396354-48396404	Caco-2	colon:	n/a
10	chr12:48396354-48396404	HRE	kidney:	n/a
11	chr12:48396354-48396404	PFSK-1	brain:	n/a
12	chr12:48396354-48396404	AG10803	skin:	n/a
13	chr12:48396354-48396404	AG04449	skin:	fetal
14	chr12:48396354-48396404	GM12892	blood:	n/a
15	chr12:48396354-48396404	SK-N-SH_RA	brain:	n/a
16	chr12:48396354-48396404	HPAEpiC	pulmonary alveolar:	n/a
17	chr12:48396354-48396404	SK-N-MC	brain:	n/a
18	chr12:48396354-48396404	NB4	blood:	n/a
19	chr12:48396354-48396404	SK-N-SH	brain:	n/a
20	chr12:48396354-48396404	HCPEpiC	choroid plexus:	n/a
21	chr12:48396354-48396404	HMEC	breast:	n/a
22	chr12:48396354-48396404	GM19239	blood:	n/a
23	chr12:48396354-48396404	K562	blood:	n/a
24	chr12:48396354-48396404	ProgFib	skin:	n/a
25	chr12:48396354-48396404	HepG2	liver:	n/a
26	chr12:48396354-48396404	HIPEpiC	eye:	n/a
27	chr12:48396354-48396404	AoSMC	blood vessel:	n/a
28	chr12:48396354-48396404	HEK293	kidney:	embryo
29	chr12:48396354-48396404	NHBE	bronchial:	n/a
30	chr12:48396354-48396404	Hepatocyte	liver:	n/a
31	chr12:48396354-48396404	ovcar-3	ovarian:	n/a
32	chr12:48396354-48396404	AG09319	gingival:	n/a
33	chr12:48396354-48396404	H1-hESC	embryonic stem cell:	embryo
34	chr12:48396354-48396404	HNPCEpiC	eye:	n/a
35	chr12:48396354-48396404	HCF	heart:	n/a
36	chr12:48396354-48396404	LNCaP	prostate:	n/a
37	chr12:48396354-48396404	SAEC	small airway:	n/a
38	chr12:48396354-48396404	PANC-1	pancreas:	n/a
39	chr12:48396354-48396404	SKMC	muscle:	n/a
40	chr12:48396354-48396404	CMK	blood:	n/a
41	chr12:48396354-48396404	AG09309	skin:	n/a
42	chr12:48396354-48396404	HRPEpiC	eye:	n/a
43	chr12:48396354-48396404	Jurkat	blood:	n/a
44	chr12:48396354-48396404	HAEpiC	amniotic membrane:	n/a
45	chr12:48396354-48396404	MCF-7	breast:	n/a
46	chr12:48396354-48396404	HCM	heart:	n/a
47	chr12:48396354-48396404	HUVEC	blood vessel:	n/a
48	chr12:48396354-48396404	NH-A	brain:	n/a
49	chr12:48396354-48396404	HCT-116	colon:	n/a
50	chr12:48396354-48396404	RPTEC	kidney:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48355944..48359601-chr12:48393326..48397759,4	MCF-7	breast:
2	chr12:48394829..48397203-chr12:48403090..48404738,2	MCF-7	breast:
3	chr12:48360987..48363483-chr12:48393695..48396604,4	MCF-7	breast:
4	chr12:48295052..48296721-chr12:48395942..48397721,2	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:

No data

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

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11168350	0.93[YRI][hapmap]
rs1793958	0.85[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1859443	0.96[YRI][hapmap]
rs7134203	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs7134878	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs7135261	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9804751	0.96[YRI][hapmap]

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
rs1635527	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48394800-48396400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48394800-48396600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
3	chr12:48394800-48396600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
4	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
6	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
7	chr12:48394800-48397000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
8	chr12:48394800-48397200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
9	chr12:48394800-48397800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:48394800-48397800	Enhancers	Spleen	Spleen
11	chr12:48394800-48398600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
12	chr12:48394800-48398800	Bivalent Enhancer	Liver	Liver
13	chr12:48394800-48399200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:48395000-48396400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:48395000-48396400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
16	chr12:48395000-48396400	Active TSS	HSMMtube	muscle
17	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
20	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
21	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
22	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Osteobl	bone
23	chr12:48395000-48396800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr12:48395000-48396800	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
27	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
29	chr12:48395000-48397000	Active TSS	Aorta	Aorta
30	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
31	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
32	chr12:48395000-48398000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:48395000-48398800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
34	chr12:48395000-48399200	Bivalent Enhancer	Fetal Thymus	thymus
35	chr12:48395200-48396400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
36	chr12:48395200-48396400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:48395200-48396600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:48395200-48396800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
39	chr12:48395200-48396800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
40	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
41	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
44	chr12:48395200-48397600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
45	chr12:48395200-48398200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
46	chr12:48395200-48398600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
47	chr12:48395200-48398800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:48395400-48396400	Flanking Active TSS	Psoas Muscle	Psoas
49	chr12:48395400-48396400	Flanking Bivalent TSS/Enh	NHLF	lung
50	chr12:48395400-48397800	Bivalent Enhancer	Stomach Mucosa	stomach

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