Variant report

Variant	rs519674
Chromosome Location	chr9:6450623-6450624
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	NR3C1	chr9:6450602-6450935	A549	lung:	n/a	n/a
2	NR3C1	chr9:6450560-6450950	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000233367	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1156870	1.00[EUR][1000 genomes]
rs56270454	1.00[EUR][1000 genomes]
rs58756210	1.00[EUR][1000 genomes]
rs59140789	1.00[EUR][1000 genomes]
rs73639304	1.00[EUR][1000 genomes]
rs73639305	1.00[EUR][1000 genomes]
rs73639306	1.00[EUR][1000 genomes]
rs73639308	1.00[EUR][1000 genomes]
rs73642515	1.00[EUR][1000 genomes]
rs73642516	1.00[EUR][1000 genomes]
rs73642517	1.00[EUR][1000 genomes]
rs73642519	1.00[EUR][1000 genomes]
rs73642521	1.00[EUR][1000 genomes]
rs7872736	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats 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	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
11	nsv1029766	chr9:6437020-6523605	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs519674	TAP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
2	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
3	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
4	chr9:6422200-6454000	Weak transcription	Fetal Lung	lung
5	chr9:6429200-6462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:6435000-6460400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:6435000-6463800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:6435400-6482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:6438000-6477600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr9:6438600-6460000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:6441600-6454600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:6441600-6475200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:6442200-6455800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:6443000-6461600	Weak transcription	HepG2	liver
15	chr9:6443600-6477600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:6445000-6461200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr9:6445600-6451200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr9:6446200-6451400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr9:6446200-6460600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:6446400-6452200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:6446600-6451200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr9:6446600-6455200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:6446800-6452200	Weak transcription	Fetal Stomach	stomach
24	chr9:6446800-6463400	Weak transcription	Fetal Intestine Large	intestine
25	chr9:6446800-6468200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr9:6447000-6455200	Weak transcription	Fetal Intestine Small	intestine
27	chr9:6447200-6450800	Genic enhancers	HUVEC	blood vessel
28	chr9:6447200-6451000	Enhancers	Brain Anterior Caudate	brain
29	chr9:6447200-6451200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr9:6447200-6463400	Weak transcription	Lung	lung
31	chr9:6447400-6450800	Enhancers	Brain Hippocampus Middle	brain
32	chr9:6447400-6451200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:6447400-6451400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr9:6448200-6454000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr9:6448600-6451000	Genic enhancers	Primary T cells from cord blood	blood
36	chr9:6448800-6450800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr9:6448800-6451000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:6448800-6451200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr9:6448800-6451200	Genic enhancers	Muscle Satellite Cultured Cells	--
40	chr9:6449000-6451000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr9:6449000-6451000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr9:6449000-6451000	Enhancers	Brain Cingulate Gyrus	brain
43	chr9:6449000-6451000	Enhancers	Brain Substantia Nigra	brain
44	chr9:6449000-6451000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr9:6449200-6450800	Genic enhancers	NHDF-Ad	bronchial
46	chr9:6449200-6451000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr9:6449200-6451000	Enhancers	A549	lung
48	chr9:6449200-6451000	Enhancers	Hela-S3	cervix
49	chr9:6449200-6452600	Enhancers	Colon Smooth Muscle	Colon
50	chr9:6449200-6454600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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