Variant report

Variant	rs12216086
Chromosome Location	chr6:4023144-4023145
allele	C/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	POLR2A	chr6:4021099-4023322	MCF10A-Er-Src	breast:	n/a	n/a
2	CHD1	chr6:4021012-4024108	IMR90	lung:	n/a	chr6:4021945-4021955
3	GATA1	chr6:4022618-4023151	PBDE	blood:	n/a	n/a
4	IRF1	chr6:4021066-4023164	K562	blood:	n/a	chr6:4022528-4022542 chr6:4022531-4022543 chr6:4023138-4023158 chr6:4023139-4023153 chr6:4022532-4022546 chr6:4023142-4023156 chr6:4022532-4022542

No.	Distal block	Cell Line	Cell type
1	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
2	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:
3	chr6:4019656..4024130-chr6:4049502..4053557,5	K562	blood:
4	chr6:4016030..4019961-chr6:4020836..4023596,5	MCF-7	breast:
5	chr6:3161756..3164171-chr6:4023037..4024626,2	K562	blood:
6	chr6:3354766..3356285-chr6:4022348..4024808,2	K562	blood:

Variant related genes	Relation type
ENSG00000230648	TF binding region
ENSG00000272248	Chromatin interaction
ENSG00000145975	Chromatin interaction
ENSG00000234817	Chromatin interaction
ENSG00000254821	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000198721	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11242896	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11962460	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1324450	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3761786	0.88[ASN][1000 genomes]
rs4266528	0.97[ASN][1000 genomes]
rs4959921	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58275491	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs644150	0.86[ASN][1000 genomes]
rs654954	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs664264	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6934443	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6937619	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs723796	0.97[ASN][1000 genomes]
rs723797	0.97[ASN][1000 genomes]
rs73721499	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73721501	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9378839	0.94[ASN][1000 genomes]
rs9378840	0.97[ASN][1000 genomes]
rs9392028	0.97[ASN][1000 genomes]
rs9392545	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9392549	1.00[ASN][1000 genomes]
rs9405695	0.97[ASN][1000 genomes]
rs9405696	0.97[ASN][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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4020000-4023200	Active TSS	HSMM	muscle
2	chr6:4020000-4023400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:4020800-4023200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:4020800-4023200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:4020800-4023200	Active TSS	Colonic Mucosa	Colon
6	chr6:4020800-4023200	Active TSS	Right Ventricle	heart
7	chr6:4020800-4023200	Active TSS	NHDF-Ad	bronchial
8	chr6:4020800-4023400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:4020800-4023600	Active TSS	Psoas Muscle	Psoas
10	chr6:4020800-4023600	Active TSS	Thymus	Thymus
11	chr6:4020800-4023600	Active TSS	A549	lung
12	chr6:4020800-4024000	Active TSS	HMEC	breast
13	chr6:4021000-4023200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr6:4021000-4023400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:4021000-4023600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:4021000-4023800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:4021000-4025000	Active TSS	GM12878-XiMat	blood
18	chr6:4021000-4025200	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr6:4021200-4023200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:4021200-4023200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:4021200-4023200	Active TSS	Aorta	Aorta
22	chr6:4021200-4023200	Active TSS	Fetal Intestine Small	intestine
23	chr6:4021200-4023600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr6:4021200-4024200	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr6:4021400-4023400	Active TSS	Fetal Thymus	thymus
26	chr6:4021800-4023400	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr6:4022000-4023400	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr6:4022000-4023600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr6:4022200-4023400	Flanking Active TSS	Liver	Liver
30	chr6:4022200-4023600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr6:4022200-4023600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:4022200-4023600	Active TSS	Right Atrium	heart
33	chr6:4022200-4023800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:4022200-4023800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:4022200-4023800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr6:4022200-4024000	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr6:4022400-4023400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:4022400-4023400	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr6:4022400-4023400	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr6:4022400-4023600	Weak transcription	Pancreas	Pancrea
41	chr6:4022400-4023800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr6:4022400-4024000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:4022400-4024000	Weak transcription	Lung	lung
44	chr6:4022400-4024000	Weak transcription	Spleen	Spleen
45	chr6:4022400-4024200	Weak transcription	Gastric	stomach
46	chr6:4022400-4025600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:4022400-4028400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:4022400-4043400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:4022600-4023200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr6:4022600-4023200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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