Variant report

Variant	rs2519080
Chromosome Location	chr9:136926136-136926137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136925619..136928594-chr9:137334503..137336256,2	K562	blood:
2	chr9:136924835..136927524-chr9:136999359..137001805,2	MCF-7	breast:
3	chr9:136912065..136915814-chr9:136924297..136928714,4	K562	blood:
4	chr9:136889886..136893006-chr9:136924602..136927881,3	MCF-7	breast:
5	chr9:136917640..136920002-chr9:136924313..136927481,4	K562	blood:
6	chr9:136924138..136926456-chr9:136992435..136994795,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196363	Chromatin interaction
ENSG00000273249	Chromatin interaction
ENSG00000235106	Chromatin interaction
ENSG00000169925	Chromatin interaction
ENSG00000235138	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10118191	0.82[AMR][1000 genomes]
rs1079524	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993895	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs1124317	0.95[CEU][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2073818	0.95[JPT][hapmap]
rs2106223	0.95[JPT][hapmap]
rs2157770	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2427946	0.85[ASN][1000 genomes]
rs2427949	0.85[ASN][1000 genomes]
rs2427950	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2427951	0.85[ASN][1000 genomes]
rs2427977	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2506696	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2506699	0.85[ASN][1000 genomes]
rs2506700	0.85[ASN][1000 genomes]
rs2506703	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2506712	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2506713	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2506714	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2519078	0.95[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2519081	0.90[CEU][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2520094	0.95[JPT][hapmap]
rs2520095	0.95[JPT][hapmap]
rs2810489	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2810491	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs3004622	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3004624	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3004626	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs408307	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs410876	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs416390	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs433402	0.95[JPT][hapmap]
rs443876	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs455381	0.95[JPT][hapmap]
rs457420	0.95[JPT][hapmap]
rs459571	0.95[JPT][hapmap]
rs460154	0.95[JPT][hapmap]
rs464024	0.88[EUR][1000 genomes]
rs464826	0.90[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs465535	0.95[JPT][hapmap]
rs465724	0.95[JPT][hapmap]
rs736902	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs756679	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv894132	chr9:136813341-136950691	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv428226	chr9:136825035-136994606	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv894135	chr9:136839840-136927657	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv894136	chr9:136839840-136938961	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv894137	chr9:136839840-136950691	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv894139	chr9:136863932-136950691	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv894140	chr9:136865879-136927657	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS 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	12 gene(s)	inside rSNPs	diseases
12	nsv894141	chr9:136865879-136938961	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv466627	chr9:136870787-136938961	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv615774	chr9:136870787-136938961	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
16	nsv894146	chr9:136874066-136938961	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	nsv894147	chr9:136874066-136950691	Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
18	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
19	nsv894149	chr9:136874158-136950691	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
20	nsv894150	chr9:136887757-136944827	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
21	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer 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 miRNA target site	57 gene(s)	inside rSNPs	diseases
22	nsv466629	chr9:136893867-136938961	Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers 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	12 gene(s)	inside rSNPs	diseases
23	nsv615779	chr9:136893867-136938961	Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
24	esv1806029	chr9:136906752-136933825	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
25	nsv430110	chr9:136909280-136964450	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
26	nsv894152	chr9:136921015-136950691	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
27	nsv466630	chr9:136925451-136991034	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
28	nsv615780	chr9:136925451-136991034	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136903600-136927000	Strong transcription	Thymus	Thymus
2	chr9:136917000-136930800	Weak transcription	K562	blood
3	chr9:136918200-136929000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:136918200-136930800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:136918400-136926200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:136918400-136926800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:136918400-136927800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr9:136918600-136930600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:136918800-136930000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:136918800-136930800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:136919000-136929000	Enhancers	Psoas Muscle	Psoas
12	chr9:136919200-136928400	Enhancers	Pancreas	Pancrea
13	chr9:136919200-136930800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:136919400-136930600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr9:136919800-136927600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr9:136919800-136930800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr9:136920000-136930800	Enhancers	Ovary	ovary
18	chr9:136920400-136928200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:136920400-136928200	Enhancers	Right Ventricle	heart
20	chr9:136920400-136929200	Genic enhancers	Fetal Intestine Small	intestine
21	chr9:136920400-136930800	Enhancers	Fetal Brain Male	brain
22	chr9:136920400-136930800	Enhancers	Left Ventricle	heart
23	chr9:136920600-136926600	Enhancers	Brain Substantia Nigra	brain
24	chr9:136920600-136927400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:136920600-136928200	Weak transcription	Dnd41	blood
26	chr9:136920600-136930800	Enhancers	Placenta	Placenta
27	chr9:136920800-136926800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:136921600-136928800	Enhancers	Colon Smooth Muscle	Colon
29	chr9:136921800-136930600	Weak transcription	NHLF	lung
30	chr9:136922000-136930400	Weak transcription	NHDF-Ad	bronchial
31	chr9:136922400-136930800	Weak transcription	A549	lung
32	chr9:136922600-136926200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:136922600-136929400	Enhancers	Adipose Nuclei	Adipose
34	chr9:136922800-136926200	Enhancers	Duodenum Mucosa	Duodenum
35	chr9:136923000-136927600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr9:136923000-136928800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr9:136923000-136929000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:136923200-136926400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:136923200-136926400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:136923400-136926600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:136923400-136926600	Enhancers	Osteobl	bone
42	chr9:136923400-136928200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:136923400-136930000	Genic enhancers	Brain Germinal Matrix	brain
44	chr9:136923400-136930600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr9:136923600-136926200	Strong transcription	Fetal Stomach	stomach
46	chr9:136923600-136926200	Weak transcription	Stomach Mucosa	stomach
47	chr9:136923600-136928200	Enhancers	Gastric	stomach
48	chr9:136923800-136926400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:136923800-136928200	Enhancers	Primary B cells from cord blood	blood
50	chr9:136923800-136930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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