Variant report

Variant	rs1635526
Chromosome Location	chr12:48396785-48396786
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	CTCF	chr12:48396700-48396850	HCPEpiC	choroid plexus:	n/a	n/a
2	CTCF	chr12:48396700-48396850	HMF	breast:	n/a	n/a
3	CTCF	chr12:48396680-48396830	HRE	kidney:	n/a	n/a
4	CTCF	chr12:48396680-48396830	AG09309	skin:	n/a	n/a
5	MAX	chr12:48396421-48397087	A549	lung:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
6	MAX	chr12:48396535-48396850	HepG2	liver:	n/a	n/a
7	SUZ12	chr12:48396098-48398262	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr12:48395778-48397117	MCF-7	breast:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
9	HA-E2F1	chr12:48395990-48397009	MCF-7	breast:	n/a	n/a
10	NRF1	chr12:48396003-48397082	SK-N-SH	brain:	n/a	n/a
11	HDAC2	chr12:48394644-48396832	MCF-7	breast:	n/a	n/a
12	BHLHE40	chr12:48396559-48396842	HepG2	liver:	n/a	n/a
13	CTCF	chr12:48396680-48396830	Caco-2	colon:	n/a	n/a
14	MAX	chr12:48396570-48396865	K562	blood:	n/a	n/a
15	CTCF	chr12:48396640-48396790	HRPEpiC	eye:	n/a	n/a
16	SETDB1	chr12:48396415-48397021	U2OS	brain:	n/a	n/a
17	MAX	chr12:48396433-48396935	HepG2	liver:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
18	CTCF	chr12:48396780-48396930	MCF-7	breast:	n/a	n/a
19	KAP1	chr12:48394655-48397087	HEK293	kidney:	n/a	n/a
20	TCF12	chr12:48396360-48397034	ECC-1	luminal epithelium:	n/a	n/a
21	MAX	chr12:48395799-48397245	A549	lung:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
22	KAP1	chr12:48396036-48397040	U2OS	brain:	n/a	n/a
23	TCF7L2	chr12:48396127-48396866	HEK293	kidney:	n/a	n/a
24	CTCF	chr12:48396700-48396850	BJ	skin:	n/a	n/a
25	SUZ12	chr12:48396473-48400031	NT2-D1	testis:	n/a	n/a
26	MXI1	chr12:48394606-48397189	SK-N-SH	brain:	n/a	n/a
27	MAX	chr12:48396319-48397210	ECC-1	luminal epithelium:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
28	MAX	chr12:48396431-48397042	HepG2	liver:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
29	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
30	CTCF	chr12:48396660-48396810	Caco-2	colon:	n/a	n/a
31	CTBP2	chr12:48394745-48396786	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48355944..48359601-chr12:48393326..48397759,4	MCF-7	breast:
2	chr12:48392370..48394865-chr12:48396464..48400282,3	K562	blood:
3	chr12:48394829..48397203-chr12:48403090..48404738,2	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	chr12:48342574..48344961-chr12:48394535..48396923,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP1-228P16.5.1-1	chr12:48396405-48396824	NONHSAT027970

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000139219	Chromatin interaction
ENSG00000134291	Chromatin interaction
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1018973	0.81[EUR][1000 genomes]
rs1034762	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs10783226	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783227	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11612578	0.85[EUR][1000 genomes]
rs1635528	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635529	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1635534	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1635535	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1635536	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1635550	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs1793912	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1793913	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1793915	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1793917	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1793931	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1793933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1793955	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1793956	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1859441	0.84[EUR][1000 genomes]
rs1859444	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990029	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3803182	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3803183	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3803184	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825404	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760611	0.80[EUR][1000 genomes]
rs4760614	0.81[EUR][1000 genomes]
rs4760615	0.83[EUR][1000 genomes]
rs4760618	0.82[EUR][1000 genomes]
rs4760677	0.81[EUR][1000 genomes]
rs6580647	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580649	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6580651	0.81[EUR][1000 genomes]
rs7132668	0.85[EUR][1000 genomes]
rs72644841	0.85[EUR][1000 genomes]
rs72644842	0.81[EUR][1000 genomes]
rs7305954	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7310579	0.83[EUR][1000 genomes]
rs7957764	0.83[EUR][1000 genomes]
rs7959755	0.81[EUR][1000 genomes]
rs7967762	0.80[EUR][1000 genomes]
rs917055	0.92[CEU][hapmap];0.80[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9651993	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9805048	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[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
rs1635526	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
3	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
4	chr12:48394800-48397000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
5	chr12:48394800-48397200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
6	chr12:48394800-48397800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:48394800-48397800	Enhancers	Spleen	Spleen
8	chr12:48394800-48398600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
9	chr12:48394800-48398800	Bivalent Enhancer	Liver	Liver
10	chr12:48394800-48399200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:48395000-48396800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr12:48395000-48396800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
15	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
17	chr12:48395000-48397000	Active TSS	Aorta	Aorta
18	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
19	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
20	chr12:48395000-48398000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:48395000-48398800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr12:48395000-48399200	Bivalent Enhancer	Fetal Thymus	thymus
23	chr12:48395200-48396800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
24	chr12:48395200-48396800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
25	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
26	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
29	chr12:48395200-48397600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
30	chr12:48395200-48398200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
31	chr12:48395200-48398600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
32	chr12:48395200-48398800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:48395400-48397800	Bivalent Enhancer	Stomach Mucosa	stomach
34	chr12:48395400-48398600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
35	chr12:48395400-48398800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:48395600-48396800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
37	chr12:48395600-48396800	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:48395600-48397000	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
39	chr12:48395600-48397000	Flanking Active TSS	Ovary	ovary
40	chr12:48395600-48397200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:48395600-48397200	Bivalent Enhancer	Small Intestine	intestine
42	chr12:48395600-48398000	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr12:48395600-48398400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:48395600-48399000	Enhancers	Pancreas	Pancrea
45	chr12:48395800-48396800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:48395800-48397000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
47	chr12:48395800-48397000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
48	chr12:48395800-48397000	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
49	chr12:48395800-48397400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
50	chr12:48395800-48397800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

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