Variant report

Variant	rs16893889
Chromosome Location	chr6:28237172-28237173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL1	chr6:28237081-28237817	HCT-116	colon:	n/a	n/a
2	GATA3	chr6:28237115-28237746	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:28237103-28237188	MCF10A-Er-Src	breast:	n/a	n/a
4	CBX3	chr6:28237082-28237723	K562	blood:	n/a	n/a
5	NFIC	chr6:28237117-28237724	SK-N-SH	brain:	n/a	n/a
6	JUN	chr6:28236993-28237755	K562	blood:	n/a	n/a
7	POLR2A	chr6:28237116-28237784	HUVEC	blood vessel:	n/a	n/a
8	JUND	chr6:28237142-28237752	SK-N-SH	brain:	n/a	chr6:28237482-28237493
9	POLR2A	chr6:28235400-28237811	K562	blood:	n/a	n/a
10	CBX3	chr6:28237110-28237786	HCT-116	colon:	n/a	n/a
11	TCF12	chr6:28237121-28237727	SK-N-SH	brain:	n/a	n/a
12	CBX3	chr6:28237055-28237751	HCT-116	colon:	n/a	n/a
13	SP1	chr6:28237113-28237828	HCT-116	colon:	n/a	n/a
14	RCOR1	chr6:28237070-28237804	IMR90	lung:	n/a	n/a
15	SP1	chr6:28237099-28237706	HCT-116	colon:	n/a	n/a
16	FOSL2	chr6:28237127-28237760	SK-N-SH	brain:	n/a	n/a
17	FOSL1	chr6:28237166-28237808	HCT-116	colon:	n/a	n/a
18	JUND	chr6:28237113-28237815	HCT-116	colon:	n/a	chr6:28237482-28237493
19	JUND	chr6:28237115-28237770	HCT-116	colon:	n/a	chr6:28237482-28237493

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28200128..28202663-chr6:28235372..28237397,2	K562	blood:
2	chr6:28232839..28237434-chr6:28303380..28305726,5	MCF-7	breast:
3	chr6:28234248..28238647-chr6:28302210..28305266,7	K562	blood:
4	chr6:28235481..28237475-chr6:28323634..28325557,2	MCF-7	breast:
5	chr6:28234029..28236350-chr6:28236563..28238803,2	K562	blood:
6	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
7	chr6:28235909..28238714-chr6:28300665..28303049,3	MCF-7	breast:
8	chr6:28217166..28222171-chr6:28233596..28237356,7	MCF-7	breast:
9	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:
10	chr6:28234828..28238066-chr6:28314810..28319280,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197062	TF binding region
ENSG00000187626	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12000	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16893947	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16893970	0.80[EUR][1000 genomes]
rs1936364	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2179174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56152789	0.82[EUR][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16893889	AL022393.7	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28235200-28239600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28235400-28239600	Weak transcription	Gastric	stomach
3	chr6:28235400-28249000	Weak transcription	Small Intestine	intestine
4	chr6:28235600-28237400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr6:28235600-28238800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:28235600-28239200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:28235600-28239200	Weak transcription	Lung	lung
8	chr6:28235600-28239600	Weak transcription	Aorta	Aorta
9	chr6:28235600-28239600	Weak transcription	Esophagus	oesophagus
10	chr6:28235600-28239600	Weak transcription	Left Ventricle	heart
11	chr6:28235600-28239800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:28235600-28239800	Weak transcription	Pancreas	Pancrea
13	chr6:28235600-28240000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:28235600-28243400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:28235600-28249000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:28235600-28249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:28235800-28238200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:28235800-28239200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:28235800-28239200	Weak transcription	Right Ventricle	heart
20	chr6:28236000-28237400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:28236000-28237800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr6:28236000-28237800	Enhancers	NHEK	skin
23	chr6:28236000-28238000	Enhancers	Hela-S3	cervix
24	chr6:28236000-28238800	Weak transcription	Fetal Stomach	stomach
25	chr6:28236000-28239200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:28236000-28239200	Weak transcription	Fetal Intestine Small	intestine
27	chr6:28236000-28239200	Weak transcription	Spleen	Spleen
28	chr6:28236000-28239400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:28236000-28239600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:28236000-28239600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:28236000-28239600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:28236000-28239600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:28236000-28239600	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:28236000-28239600	Weak transcription	Placenta	Placenta
35	chr6:28236000-28239600	Weak transcription	Fetal Thymus	thymus
36	chr6:28236000-28239600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:28236000-28239600	Weak transcription	Thymus	Thymus
38	chr6:28236000-28239600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr6:28236000-28239800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:28236000-28239800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:28236000-28239800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:28236200-28237400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:28236200-28237400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:28236200-28238800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:28236200-28239200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:28236200-28239200	Weak transcription	Brain Anterior Caudate	brain
47	chr6:28236200-28239400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr6:28236200-28239600	Weak transcription	Primary B cells from cord blood	blood
49	chr6:28236200-28239600	Weak transcription	Brain Substantia Nigra	brain
50	chr6:28236200-28239600	Weak transcription	Rectal Mucosa Donor 31	rectum

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