Variant report

Variant	rs28599555
Chromosome Location	chr16:48369825-48369826
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	CEBPB	chr16:48369810-48370265	IMR90	lung:	n/a	n/a
2	POLR2A	chr16:48369698-48370340	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:48365435..48368330-chr16:48369439..48371339,2	K562	blood:
2	chr16:48365435..48368330-chr16:48369439..48371556,3	K562	blood:

Variant related genes	Relation type
UBA52P8	TF binding region
ENSG00000102910	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12102896	0.86[AFR][1000 genomes]
rs13332870	1.00[AMR][1000 genomes]
rs13335175	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13336203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13336441	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13336832	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13337923	1.00[AMR][1000 genomes]
rs28361908	1.00[AMR][1000 genomes]
rs28379458	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28473019	1.00[AMR][1000 genomes]
rs28539217	1.00[AMR][1000 genomes]
rs28661941	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28848294	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9922477	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926437	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926749	1.00[AMR][1000 genomes]
rs9927124	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928527	1.00[AMR][1000 genomes]
rs9929780	1.00[AMR][1000 genomes]
rs9931267	1.00[AMR][1000 genomes]
rs9931866	1.00[AMR][1000 genomes]
rs9932677	1.00[AMR][1000 genomes]
rs9933958	1.00[AMR][1000 genomes]
rs9934175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9934459	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9934918	1.00[AMR][1000 genomes]
rs9936494	1.00[AMR][1000 genomes]
rs9936636	1.00[AMR][1000 genomes]
rs9936892	1.00[AMR][1000 genomes]
rs9938115	1.00[AMR][1000 genomes]
rs9938350	1.00[AMR][1000 genomes]
rs9938594	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9940237	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9941354	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
2	esv1821072	chr16:48268318-48504364	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv833219	chr16:48290595-48459301	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1061708	chr16:48304343-48482594	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv542917	chr16:48304343-48482594	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv2758424	chr16:48329437-48479754	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv2758645	chr16:48329437-48479754	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS 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	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48338600-48381200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr16:48343400-48375600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr16:48347600-48384800	Weak transcription	Fetal Kidney	kidney
4	chr16:48352200-48395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:48355800-48375800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr16:48355800-48384800	Weak transcription	Small Intestine	intestine
7	chr16:48363400-48383400	Weak transcription	HUVEC	blood vessel
8	chr16:48364400-48378800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr16:48365000-48381400	Weak transcription	Pancreas	Pancrea
10	chr16:48365000-48388200	Weak transcription	Right Atrium	heart
11	chr16:48365200-48378600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr16:48365200-48392400	Strong transcription	Liver	Liver
13	chr16:48365800-48377600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr16:48366200-48371400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr16:48366400-48377400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:48366600-48372600	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr16:48366800-48377400	Strong transcription	Dnd41	blood
18	chr16:48367000-48370400	Strong transcription	Brain Angular Gyrus	brain
19	chr16:48367000-48378600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr16:48367000-48387000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr16:48367200-48370400	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr16:48367200-48372600	Strong transcription	Fetal Muscle Leg	muscle
23	chr16:48367200-48387000	Strong transcription	Primary T cells from cord blood	blood
24	chr16:48367400-48372400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr16:48367400-48372400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr16:48367400-48378600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr16:48367400-48387000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr16:48367600-48370000	Strong transcription	GM12878-XiMat	blood
29	chr16:48367600-48370400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr16:48367600-48377000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr16:48367600-48377400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr16:48367600-48378200	Strong transcription	Primary B cells from cord blood	blood
33	chr16:48367600-48378600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr16:48367600-48378800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr16:48367800-48370000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr16:48367800-48370400	Strong transcription	Brain Anterior Caudate	brain
37	chr16:48367800-48370400	Strong transcription	Fetal Lung	lung
38	chr16:48367800-48372800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr16:48367800-48373400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr16:48367800-48374400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr16:48367800-48377200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr16:48367800-48377200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr16:48367800-48378600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr16:48367800-48387200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr16:48368000-48370000	Strong transcription	Hela-S3	cervix
46	chr16:48368000-48370200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr16:48368000-48370200	Strong transcription	Rectal Smooth Muscle	rectum
48	chr16:48368000-48370400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr16:48368000-48370400	Strong transcription	Fetal Thymus	thymus
50	chr16:48368000-48371400	Strong transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links