Variant report

Variant	rs28496446
Chromosome Location	chr4:16207805-16207806
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	CTCF	chr4:16207660-16207810	HRPEpiC	eye:	n/a	n/a
2	MYC	chr4:16207255-16207905	MCF10A-Er-Src	breast:	n/a	chr4:16207433-16207441
3	MYC	chr4:16207211-16207850	MCF10A-Er-Src	breast:	n/a	chr4:16207433-16207441
4	CTCF	chr4:16207053-16207896	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:16207543..16210716-chr4:16226514..16229225,4	K562	blood:
2	chr4:16205687..16210095-chr4:16211514..16215415,4	K562	blood:
3	chr4:16206563..16211517-chr4:16224602..16229225,6	K562	blood:
4	chr4:16202184..16204166-chr4:16205762..16207815,2	K562	blood:
5	chr4:16204628..16208605-chr4:16216498..16220405,4	K562	blood:

Variant related genes	Relation type
TAPT1	TF binding region
ENSG00000263327	Chromatin interaction
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10007592	0.95[ASN][1000 genomes]
rs10017532	0.83[AFR][1000 genomes]
rs10516296	0.95[ASN][1000 genomes]
rs11946259	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1373109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443368	0.92[EUR][1000 genomes]
rs1443369	0.92[EUR][1000 genomes]
rs1443370	0.92[EUR][1000 genomes]
rs1621739	0.83[AFR][1000 genomes]
rs1712479	0.92[EUR][1000 genomes]
rs17479949	0.94[EUR][1000 genomes]
rs2011754	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028631	0.84[AFR][1000 genomes]
rs28377010	0.96[EUR][1000 genomes]
rs28403341	0.95[ASN][1000 genomes]
rs28427433	0.82[AFR][1000 genomes]
rs28481627	0.95[ASN][1000 genomes]
rs28485928	0.98[EUR][1000 genomes]
rs28517428	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28537328	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28654954	0.82[AFR][1000 genomes]
rs28726676	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28757814	0.90[ASN][1000 genomes]
rs317852	0.81[AFR][1000 genomes]
rs317858	0.94[EUR][1000 genomes]
rs317864	0.81[AFR][1000 genomes]
rs35046072	0.91[EUR][1000 genomes]
rs35367114	0.87[EUR][1000 genomes]
rs35931597	0.86[AFR][1000 genomes]
rs4235382	0.86[AFR][1000 genomes]
rs4501221	0.81[AFR][1000 genomes]
rs57110573	0.95[ASN][1000 genomes]
rs58468710	0.95[ASN][1000 genomes]
rs6823623	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73798865	0.95[ASN][1000 genomes]
rs73798866	0.95[ASN][1000 genomes]
rs73798869	0.95[ASN][1000 genomes]
rs73798871	0.86[ASN][1000 genomes]
rs73798874	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73798875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73798883	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73802012	0.81[ASN][1000 genomes]
rs7664407	0.95[ASN][1000 genomes]
rs7690701	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs961450	0.92[EUR][1000 genomes]
rs975229	0.92[EUR][1000 genomes]
rs9995025	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16168000-16208000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:16168000-16213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:16170800-16208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
5	chr4:16193000-16208200	Weak transcription	Esophagus	oesophagus
6	chr4:16193000-16216000	Weak transcription	Spleen	Spleen
7	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
8	chr4:16193200-16208000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:16193200-16208000	Weak transcription	Lung	lung
10	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
11	chr4:16193400-16211200	Weak transcription	Placenta	Placenta
12	chr4:16193600-16208600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:16198600-16211200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:16198600-16216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:16198600-16221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:16198600-16222400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:16198800-16211400	Weak transcription	Aorta	Aorta
18	chr4:16198800-16218800	Weak transcription	HSMM	muscle
19	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:16198800-16226000	Weak transcription	NHEK	skin
21	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:16199800-16208000	Weak transcription	Small Intestine	intestine
23	chr4:16199800-16209800	Weak transcription	NHLF	lung
24	chr4:16199800-16215800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:16200000-16208600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:16200000-16214200	Weak transcription	Fetal Heart	heart
27	chr4:16200200-16209000	Weak transcription	NHDF-Ad	bronchial
28	chr4:16200800-16213600	Weak transcription	HUVEC	blood vessel
29	chr4:16200800-16214800	Weak transcription	Stomach Mucosa	stomach
30	chr4:16200800-16218000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:16202200-16208000	Weak transcription	Fetal Stomach	stomach
32	chr4:16202600-16208200	Strong transcription	Dnd41	blood
33	chr4:16202800-16220800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:16203600-16208000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:16203600-16209600	Enhancers	Brain Anterior Caudate	brain
36	chr4:16203800-16208000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr4:16203800-16211200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:16204200-16213800	Weak transcription	Ovary	ovary
39	chr4:16204400-16209800	Enhancers	Brain Substantia Nigra	brain
40	chr4:16204600-16209600	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr4:16204600-16210400	Enhancers	Brain Angular Gyrus	brain
42	chr4:16204800-16210800	Enhancers	Brain Hippocampus Middle	brain
43	chr4:16204800-16226600	Weak transcription	NH-A	brain
44	chr4:16205000-16209400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:16205200-16208000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr4:16205200-16225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:16205400-16208000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:16205800-16211600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:16206000-16208600	Strong transcription	Fetal Intestine Small	intestine
50	chr4:16206000-16211200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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