Variant report

Variant	rs2519799
Chromosome Location	chr9:136810857-136810858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136809714..136811790-chr9:136818542..136820175,2	MCF-7	breast:
2	chr9:136810315..136812430-chr9:136853875..136857440,3	MCF-7	breast:
3	chr9:136810410..136813300-chr9:136824316..136826699,2	MCF-7	breast:
4	chr9:136810475..136813039-chr9:136813457..136816106,3	K562	blood:
5	chr9:136809945..136812192-chr9:136855956..136857665,2	MCF-7	breast:
6	chr9:136809153..136811030-chr9:136812692..136814573,2	MCF-7	breast:
7	chr9:136799983..136801681-chr9:136809502..136811827,2	MCF-7	breast:
8	chr9:136747124..136749714-chr9:136809806..136812182,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs2073829	0.82[JPT][hapmap]
rs2073885	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2077384	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2263807	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2428004	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2519102	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2519103	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2519104	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2519106	1.00[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2519107	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2519108	0.82[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2519109	0.82[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2519111	0.91[CEU][hapmap]
rs2519112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2519802	0.90[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2519803	0.82[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2519804	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2519805	1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2789848	0.94[ASN][1000 genomes]
rs2789850	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2789851	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2789852	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810530	0.88[ASN][1000 genomes]
rs2810531	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2810532	0.80[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2810533	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2810534	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs886018	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv894127	chr9:136747832-136811772	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv894128	chr9:136753246-136906752	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1046310	chr9:136762829-136872226	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv894130	chr9:136767346-136906752	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv831748	chr9:136788484-136944326	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats 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	30 gene(s)	inside rSNPs	diseases
9	nsv894131	chr9:136792765-136906752	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv466626	chr9:136807770-136835343	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv615742	chr9:136807770-136835343	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv831749	chr9:136809200-136915764	Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2519799	BRD3	cis	parietal	SCAN
rs2519799	GTF3C5	cis	cerebellum	SCAN
rs2519799	C9orf98	cis	cerebellum	SCAN
rs2519799	ABL1	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136753000-136813200	Weak transcription	Aorta	Aorta
2	chr9:136784000-136819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:136797800-136811000	Weak transcription	A549	lung
4	chr9:136801000-136815400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:136801200-136815600	Weak transcription	Right Atrium	heart
6	chr9:136801200-136815800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:136801200-136820200	Weak transcription	Left Ventricle	heart
8	chr9:136801400-136821200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:136802000-136815800	Weak transcription	Colonic Mucosa	Colon
10	chr9:136802200-136815800	Strong transcription	Fetal Intestine Small	intestine
11	chr9:136802800-136816200	Weak transcription	Fetal Kidney	kidney
12	chr9:136803000-136813000	Weak transcription	Fetal Lung	lung
13	chr9:136803000-136815200	Weak transcription	HSMMtube	muscle
14	chr9:136803200-136811200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr9:136803200-136821200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:136803400-136811000	Weak transcription	Hela-S3	cervix
17	chr9:136803600-136821000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:136804200-136813400	Weak transcription	Gastric	stomach
19	chr9:136804200-136815400	Weak transcription	Ovary	ovary
20	chr9:136804200-136815400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr9:136804200-136819800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:136804200-136820200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:136804200-136821000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:136804200-136821200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr9:136804400-136814800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:136804400-136815000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:136805200-136811000	Weak transcription	HepG2	liver
28	chr9:136805600-136811200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:136805800-136811000	Weak transcription	Right Ventricle	heart
30	chr9:136805800-136819400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:136806200-136813000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr9:136807400-136813400	Strong transcription	Fetal Stomach	stomach
33	chr9:136807600-136813400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr9:136808000-136811200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:136808000-136811200	Enhancers	Pancreas	Pancrea
36	chr9:136808400-136811800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr9:136808400-136815600	Weak transcription	Brain Angular Gyrus	brain
38	chr9:136808600-136811400	Enhancers	NH-A	brain
39	chr9:136808600-136813400	Enhancers	Primary B cells from peripheral blood	blood
40	chr9:136808800-136811400	Enhancers	HMEC	breast
41	chr9:136808800-136813600	Enhancers	Primary B cells from cord blood	blood
42	chr9:136809000-136811800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:136809000-136812200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:136809200-136811200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr9:136809200-136814200	Enhancers	HUVEC	blood vessel
46	chr9:136809400-136811000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:136809400-136811400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:136809400-136812200	Enhancers	Spleen	Spleen
49	chr9:136809600-136811000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
50	chr9:136809600-136811800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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