Variant report

Variant	rs4254150
Chromosome Location	chr12:105478678-105478679
allele	G/T
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	SIN3AK20	chr12:105477975-105478714	SK-N-SH	brain:	n/a	n/a
2	ELF1	chr12:105477993-105478723	GM12878	blood:	n/a	chr12:105478242-105478251
3	CTCF	chr12:105478660-105478810	HepG2	liver:	n/a	n/a
4	TCF12	chr12:105477456-105478709	ECC-1	luminal epithelium:	n/a	n/a
5	MAZ	chr12:105477239-105478787	IMR90	lung:	n/a	chr12:105477508-105477517
6	SIN3A	chr12:105477501-105478776	H1-hESC	embryonic stem cell:	n/a	chr12:105477593-105477602 chr12:105478243-105478254 chr12:105478538-105478551 chr12:105478505-105478516 chr12:105478572-105478585 chr12:105478384-105478397
7	MAX	chr12:105477994-105478710	H1-hESC	embryonic stem cell:	n/a	n/a
8	SMARCB1	chr12:105477507-105478751	Hela-S3	cervix:	n/a	n/a
9	MAX	chr12:105477970-105478682	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr12:105476576-105478872	SK-N-SH	brain:	n/a	chr12:105477034-105477043 chr12:105477194-105477209
11	RFX5	chr12:105478621-105478695	HepG2	liver:	n/a	n/a
12	FOXA2	chr12:105477886-105478743	A549	lung:	n/a	n/a
13	HMGN3	chr12:105478096-105478698	K562	blood:	n/a	n/a
14	MAX	chr12:105476774-105478777	ECC-1	luminal epithelium:	n/a	chr12:105477033-105477042 chr12:105477032-105477043 chr12:105477508-105477517 chr12:105477032-105477043 chr12:105477028-105477047 chr12:105477032-105477042 chr12:105477032-105477042 chr12:105477033-105477042 chr12:105477033-105477042 chr12:105477032-105477043 chr12:105477031-105477046
15	MXI1	chr12:105476864-105478845	IMR90	lung:	n/a	chr12:105477034-105477043 chr12:105477194-105477209
16	MAX	chr12:105478002-105478679	HepG2	liver:	n/a	n/a
17	ZNF143	chr12:105478194-105478699	H1-hESC	embryonic stem cell:	n/a	n/a
18	TCF3	chr12:105478087-105478721	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:105478673-105478735	Gliobla	brain:	n/a	n/a
20	SP1	chr12:105478168-105478690	A549	lung:	n/a	chr12:105478388-105478397 chr12:105478667-105478680
21	MAX	chr12:105477886-105478716	A549	lung:	n/a	n/a
22	E2F6	chr12:105477503-105478776	H1-hESC	embryonic stem cell:	n/a	chr12:105478098-105478110
23	MAX	chr12:105476770-105478839	A549	lung:	n/a	chr12:105477033-105477042 chr12:105477032-105477043 chr12:105477508-105477517 chr12:105477032-105477043 chr12:105477028-105477047 chr12:105477032-105477042 chr12:105477032-105477042 chr12:105477033-105477042 chr12:105477033-105477042 chr12:105477032-105477043 chr12:105477031-105477046
24	CCNT2	chr12:105478088-105478692	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:105476762..105478986-chr12:105499431..105503042,4	K562	blood:
2	chr12:105476808..105479481-chr12:105501524..105503382,3	K562	blood:
3	chr12:105477772..105479851-chr12:105501425..105505225,4	MCF-7	breast:
4	chr12:105477899..105479847-chr12:105501301..105502988,2	MCF-7	breast:

Variant related genes	Relation type
ALDH1L2	TF binding region
ENSG00000257999	Chromatin interaction
ENSG00000136051	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17036637	0.87[AFR][1000 genomes]
rs59124570	0.83[AFR][1000 genomes]
rs7300384	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393847	1.00[AMR][1000 genomes]
rs73393854	1.00[AMR][1000 genomes]
rs73393861	1.00[AMR][1000 genomes]
rs73393887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73395712	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105477000-105478800	Active TSS	Brain Angular Gyrus	brain
2	chr12:105477200-105478800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:105477200-105478800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:105477200-105478800	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr12:105477200-105478800	Active TSS	HSMM	muscle
6	chr12:105477200-105479000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr12:105477400-105478800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr12:105477400-105478800	Active TSS	Brain Cingulate Gyrus	brain
9	chr12:105477400-105478800	Active TSS	Brain Germinal Matrix	brain
10	chr12:105477400-105478800	Active TSS	Brain Hippocampus Middle	brain
11	chr12:105477400-105478800	Active TSS	NHLF	lung
12	chr12:105477600-105478800	Active TSS	Gastric	stomach
13	chr12:105477600-105478800	Enhancers	Spleen	Spleen
14	chr12:105477800-105478800	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr12:105478000-105478800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:105478000-105478800	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr12:105478000-105478800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr12:105478000-105478800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr12:105478000-105478800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:105478000-105478800	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr12:105478000-105478800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr12:105478000-105478800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:105478000-105478800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:105478000-105478800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:105478000-105478800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:105478000-105478800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:105478000-105478800	Active TSS	Brain Anterior Caudate	brain
28	chr12:105478000-105478800	Active TSS	Duodenum Mucosa	Duodenum
29	chr12:105478000-105478800	Active TSS	Fetal Kidney	kidney
30	chr12:105478000-105478800	Active TSS	Lung	lung
31	chr12:105478000-105478800	Active TSS	Rectal Smooth Muscle	rectum
32	chr12:105478000-105478800	Active TSS	A549	lung
33	chr12:105478000-105478800	Active TSS	HepG2	liver
34	chr12:105478000-105478800	Active TSS	HUVEC	blood vessel
35	chr12:105478000-105478800	Active TSS	K562	blood
36	chr12:105478000-105478800	Active TSS	NH-A	brain
37	chr12:105478000-105478800	Active TSS	NHEK	skin
38	chr12:105478000-105478800	Active TSS	Osteobl	bone
39	chr12:105478000-105479400	Enhancers	Fetal Brain Male	brain
40	chr12:105478200-105478800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr12:105478200-105478800	Enhancers	Primary B cells from peripheral blood	blood
42	chr12:105478200-105478800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr12:105478200-105478800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:105478200-105478800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:105478200-105478800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr12:105478200-105479000	Enhancers	Placenta	Placenta
47	chr12:105478400-105478800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:105478400-105478800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:105478400-105478800	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr12:105478400-105478800	Active TSS	Colonic Mucosa	Colon

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