Variant report

Variant	rs28726676
Chromosome Location	chr4:16196682-16196683
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	GATA3	chr4:16196667-16197041	T-47D	breast:	n/a	chr4:16196870-16196877 chr4:16196870-16196882 chr4:16196868-16196884

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:16194161..16197460-chr4:16224313..16229621,5	K562	blood:

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

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10007592	0.95[ASN][1000 genomes]
rs10017532	0.80[AFR][1000 genomes]
rs10516296	0.95[ASN][1000 genomes]
rs11946259	0.95[ASN][1000 genomes]
rs1373109	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443368	0.90[EUR][1000 genomes]
rs1443369	0.90[EUR][1000 genomes]
rs1443370	0.90[EUR][1000 genomes]
rs1621739	0.86[AFR][1000 genomes]
rs1662651	0.80[AFR][1000 genomes]
rs1712479	0.94[EUR][1000 genomes]
rs17479949	0.96[EUR][1000 genomes]
rs2011754	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028631	0.81[AFR][1000 genomes]
rs28377010	0.94[EUR][1000 genomes]
rs28403341	0.95[ASN][1000 genomes]
rs28427433	0.85[AFR][1000 genomes]
rs28481627	0.95[ASN][1000 genomes]
rs28485928	0.96[EUR][1000 genomes]
rs28496446	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28517428	0.95[ASN][1000 genomes]
rs28537328	0.95[ASN][1000 genomes]
rs28757814	0.90[ASN][1000 genomes]
rs317852	0.84[AFR][1000 genomes]
rs317858	0.96[EUR][1000 genomes]
rs35046072	0.89[EUR][1000 genomes]
rs35367114	0.89[EUR][1000 genomes]
rs35931597	0.83[AFR][1000 genomes]
rs4235382	0.83[AFR][1000 genomes]
rs4501221	0.84[AFR][1000 genomes]
rs57110573	0.95[ASN][1000 genomes]
rs58468710	0.95[ASN][1000 genomes]
rs6823623	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	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73798875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73798883	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73802012	0.81[ASN][1000 genomes]
rs7664407	0.95[ASN][1000 genomes]
rs7690701	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs961450	0.90[EUR][1000 genomes]
rs975229	0.94[EUR][1000 genomes]
rs9995025	0.83[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:121 , 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	chr4:16168200-16198000	Weak transcription	A549	lung
4	chr4:16168400-16197800	Weak transcription	NHLF	lung
5	chr4:16168400-16198000	Weak transcription	NH-A	brain
6	chr4:16168600-16198000	Weak transcription	NHEK	skin
7	chr4:16170800-16208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:16171400-16207200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:16171600-16198000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:16172000-16198000	Weak transcription	HSMMtube	muscle
11	chr4:16174400-16196800	Weak transcription	Stomach Mucosa	stomach
12	chr4:16176200-16198000	Weak transcription	HSMM	muscle
13	chr4:16181000-16197800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:16181000-16197800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
16	chr4:16184200-16197600	Strong transcription	Primary B cells from cord blood	blood
17	chr4:16184200-16198000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:16184200-16200600	Strong transcription	Fetal Thymus	thymus
19	chr4:16185400-16197400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:16185600-16197600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:16186200-16197400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr4:16186400-16197600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:16186800-16198000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:16187400-16199600	Weak transcription	Hela-S3	cervix
25	chr4:16188200-16197800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:16188800-16197800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:16189000-16197800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:16190600-16198000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:16190800-16196800	Strong transcription	Primary T cells from cord blood	blood
30	chr4:16191400-16207000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr4:16191600-16198200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:16191800-16197800	Weak transcription	NHDF-Ad	bronchial
33	chr4:16191800-16198000	Weak transcription	Fetal Kidney	kidney
34	chr4:16192000-16198200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:16192200-16198000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:16192200-16204800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:16192800-16198000	Weak transcription	GM12878-XiMat	blood
38	chr4:16193000-16196800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:16193000-16197800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:16193000-16197800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:16193000-16198000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr4:16193000-16198000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:16193000-16198000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:16193000-16198000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:16193000-16198400	Weak transcription	Psoas Muscle	Psoas
46	chr4:16193000-16205000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr4:16193000-16207600	Weak transcription	Brain Germinal Matrix	brain
48	chr4:16193000-16208200	Weak transcription	Esophagus	oesophagus
49	chr4:16193000-16216000	Weak transcription	Spleen	Spleen
50	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon

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