Variant report

Variant	rs16904262
Chromosome Location	chr8:131417543-131417544
allele	A/G
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	PBX3	chr8:131416739-131417621	SK-N-SH	brain:	n/a	n/a
2	JUND	chr8:131416732-131417578	SK-N-SH	brain:	n/a	chr8:131416896-131416903
3	PBX3	chr8:131416797-131417630	SK-N-SH	brain:	n/a	n/a
4	FOSL2	chr8:131416835-131417572	SK-N-SH	brain:	n/a	chr8:131416896-131416903
5	NFIC	chr8:131416745-131417681	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr8:131416705-131417590	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr8:131416523-131417724	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr8:131416675-131417612	SK-N-SH	brain:	n/a	chr8:131417244-131417252
9	RXRA	chr8:131416813-131417592	SK-N-SH	brain:	n/a	n/a
10	EP300	chr8:131416729-131417659	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr8:131416415-131417715	SK-N-SH	brain:	n/a	chr8:131417244-131417252 chr8:131416466-131416476

Variant related genes	Relation type
ASAP1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16904226	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16904259	1.00[YRI][hapmap]
rs16904271	1.00[AMR][1000 genomes]
rs16904273	1.00[AMR][1000 genomes]
rs16904275	1.00[AMR][1000 genomes]
rs16904276	1.00[AMR][1000 genomes]
rs16904277	1.00[AMR][1000 genomes]
rs16904278	1.00[AMR][1000 genomes]
rs16904280	1.00[AMR][1000 genomes]
rs16904281	1.00[AMR][1000 genomes]
rs6984626	1.00[AMR][1000 genomes]
rs6988717	1.00[AMR][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	nsv869334	chr8:131025093-131651487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv915580	chr8:131025093-131667578	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv533085	chr8:131042781-131755007	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16904262	MAN2A1	trans	lymphoblastoid	seeQTL
rs16904262	NR2F2	trans	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:131371600-131419800	Weak transcription	Aorta	Aorta
2	chr8:131395600-131434200	Weak transcription	Hela-S3	cervix
3	chr8:131399400-131419600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:131401600-131421800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:131402600-131418000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:131405600-131422800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:131405600-131423600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr8:131407400-131419600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr8:131407800-131419400	Weak transcription	Spleen	Spleen
10	chr8:131408000-131422200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr8:131409200-131422400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:131409200-131424000	Weak transcription	Right Ventricle	heart
13	chr8:131409200-131426400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr8:131409200-131431800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr8:131409400-131421800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr8:131409600-131428400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr8:131410000-131423200	Weak transcription	Adipose Nuclei	Adipose
18	chr8:131410000-131423200	Weak transcription	Ovary	ovary
19	chr8:131411200-131420400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:131411400-131418400	Weak transcription	Fetal Lung	lung
21	chr8:131411400-131419400	Weak transcription	Left Ventricle	heart
22	chr8:131412600-131417600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr8:131414000-131417600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr8:131414400-131431400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr8:131414600-131419400	Weak transcription	Brain Anterior Caudate	brain
26	chr8:131414600-131422000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr8:131414600-131431000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr8:131414800-131422000	Weak transcription	Fetal Heart	heart
29	chr8:131415200-131420400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:131416200-131418000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:131416200-131418000	Strong transcription	A549	lung
32	chr8:131416400-131417600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr8:131416400-131418000	Enhancers	Osteobl	bone
34	chr8:131416600-131417600	Enhancers	HSMMtube	muscle
35	chr8:131416600-131418000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr8:131416600-131418000	Enhancers	HSMM	muscle
37	chr8:131416600-131418000	Enhancers	NHDF-Ad	bronchial
38	chr8:131416600-131419600	Genic enhancers	HUVEC	blood vessel
39	chr8:131416600-131420600	Enhancers	NHLF	lung
40	chr8:131416800-131417800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr8:131416800-131418000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr8:131416800-131418000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr8:131416800-131418000	Enhancers	Right Atrium	heart
44	chr8:131416800-131418000	Strong transcription	HepG2	liver
45	chr8:131417000-131417600	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr8:131417000-131417800	Enhancers	Psoas Muscle	Psoas
47	chr8:131417000-131417800	Enhancers	HMEC	breast
48	chr8:131417000-131418000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr8:131417000-131418000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr8:131417000-131418000	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links