Variant report

Variant	rs1793931
Chromosome Location	chr12:48396505-48396506
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	MAX	chr12:48396421-48397087	A549	lung:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
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	SETDB1	chr12:48396415-48397021	U2OS	brain:	n/a	n/a
8	MAX	chr12:48396433-48396935	HepG2	liver:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
9	KAP1	chr12:48394655-48397087	HEK293	kidney:	n/a	n/a
10	TCF12	chr12:48396360-48397034	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr12:48395799-48397245	A549	lung:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
12	KAP1	chr12:48396036-48397040	U2OS	brain:	n/a	n/a
13	TCF7L2	chr12:48396127-48396866	HEK293	kidney:	n/a	n/a
14	SUZ12	chr12:48396473-48400031	NT2-D1	testis:	n/a	n/a
15	MXI1	chr12:48394606-48397189	SK-N-SH	brain:	n/a	n/a
16	MAX	chr12:48396319-48397210	ECC-1	luminal epithelium:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
17	MAX	chr12:48396431-48397042	HepG2	liver:	n/a	chr12:48396876-48396883 chr12:48396875-48396884 chr12:48396872-48396887
18	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
19	CTCF	chr12:48396460-48396610	SK-N-SH_RA	brain:	n/a	n/a
20	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	chr12:48360987..48363483-chr12:48393695..48396604,4	MCF-7	breast:
5	chr12:48295052..48296721-chr12:48395942..48397721,2	MCF-7	breast:
6	chr12:48393252..48397718-chr12:48414474..48419166,5	MCF-7	breast:
7	chr12:48393914..48396723-chr12:48402943..48405805,2	K562	blood:
8	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
ENSG00000258203	Chromatin interaction
ENSG00000134291	Chromatin interaction
ENSG00000257955	Chromatin interaction
ENSG00000257985	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	0.83[EUR][1000 genomes]
rs1034762	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs10783226	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783227	0.86[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11612578	0.87[EUR][1000 genomes]
rs1635526	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]
rs1635528	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635529	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635534	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1635535	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1635536	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1635550	0.80[CEU][hapmap]
rs1793912	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1793913	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1793915	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1793917	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1793933	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793955	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793956	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1859441	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs1859444	0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1990029	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3803182	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3803183	0.82[CHB][hapmap];0.83[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803184	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825404	0.94[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760611	0.82[EUR][1000 genomes]
rs4760614	0.83[EUR][1000 genomes]
rs4760615	0.85[EUR][1000 genomes]
rs4760618	0.84[EUR][1000 genomes]
rs4760677	0.83[EUR][1000 genomes]
rs6580647	0.94[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580649	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs6580651	0.83[EUR][1000 genomes]
rs7132668	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72644841	0.87[EUR][1000 genomes]
rs72644842	0.83[EUR][1000 genomes]
rs7305954	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7310579	0.85[EUR][1000 genomes]
rs7957764	0.85[EUR][1000 genomes]
rs7959755	0.83[EUR][1000 genomes]
rs7967762	0.82[EUR][1000 genomes]
rs917055	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9651993	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9805048	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[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
rs1793931	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	chr12:48394800-48396600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
2	chr12:48394800-48396600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
3	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
5	chr12:48394800-48396800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
6	chr12:48394800-48397000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
7	chr12:48394800-48397200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
8	chr12:48394800-48397800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:48394800-48397800	Enhancers	Spleen	Spleen
10	chr12:48394800-48398600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
11	chr12:48394800-48398800	Bivalent Enhancer	Liver	Liver
12	chr12:48394800-48399200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
16	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
17	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
18	chr12:48395000-48396600	Flanking Bivalent TSS/Enh	Osteobl	bone
19	chr12:48395000-48396800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:48395000-48396800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
23	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
24	chr12:48395000-48396800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
25	chr12:48395000-48397000	Active TSS	Aorta	Aorta
26	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
27	chr12:48395000-48397000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
28	chr12:48395000-48398000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:48395000-48398800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr12:48395000-48399200	Bivalent Enhancer	Fetal Thymus	thymus
31	chr12:48395200-48396600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:48395200-48396800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
33	chr12:48395200-48396800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
34	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
35	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:48395200-48397000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
38	chr12:48395200-48397600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr12:48395200-48398200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
40	chr12:48395200-48398600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
41	chr12:48395200-48398800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:48395400-48397800	Bivalent Enhancer	Stomach Mucosa	stomach
43	chr12:48395400-48398600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
44	chr12:48395400-48398800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:48395600-48396600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:48395600-48396800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
47	chr12:48395600-48396800	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:48395600-48397000	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
49	chr12:48395600-48397000	Flanking Active TSS	Ovary	ovary
50	chr12:48395600-48397200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

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