Variant report

Variant	rs2260095
Chromosome Location	chr9:136705956-136705957
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136693193..136695419-chr9:136705719..136708043,2	MCF-7	breast:
2	chr9:136701985..136719064-chr9:136732605..136742545,35	MCF-7	breast:
3	chr9:136705845..136709816-chr9:136855790..136859235,6	MCF-7	breast:
4	chr9:136657846..136660757-chr9:136705062..136707156,2	MCF-7	breast:
5	chr9:136700961..136707109-chr9:136726164..136730903,8	MCF-7	breast:
6	chr9:136683947..136686001-chr9:136705549..136707591,2	MCF-7	breast:
7	chr9:136700981..136702843-chr9:136704343..136707980,3	MCF-7	breast:
8	chr9:136697564..136700865-chr9:136704214..136707852,3	MCF-7	breast:
9	chr9:136705778..136709995-chr9:136855858..136859716,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10821526	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10821527	0.82[CEU][hapmap]
rs10993820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10993822	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10993823	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10993824	0.93[ASN][1000 genomes]
rs10993826	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10993828	0.93[ASN][1000 genomes]
rs10993829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10993830	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10993832	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12000549	0.95[ASN][1000 genomes]
rs12005762	0.95[ASN][1000 genomes]
rs12341505	0.86[ASN][1000 genomes]
rs12377799	0.93[ASN][1000 genomes]
rs1557679	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17663678	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2073830	0.82[CEU][hapmap]
rs2073928	0.84[ASN][1000 genomes]
rs2073929	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2073930	0.91[ASN][1000 genomes]
rs2156323	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2261150	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2428123	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2428124	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2428126	0.84[ASN][1000 genomes]
rs2428129	0.84[ASN][1000 genomes]
rs2486350	0.82[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2486351	0.94[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2502765	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2510238	0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2510254	0.94[CEU][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs28436700	0.84[ASN][1000 genomes]
rs35711919	0.93[ASN][1000 genomes]
rs35776936	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3780737	0.81[CEU][hapmap]
rs3819500	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3819502	0.94[CEU][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3819503	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs3819504	0.93[ASN][1000 genomes]
rs3819505	0.93[ASN][1000 genomes]
rs55646136	0.93[ASN][1000 genomes]
rs55939286	1.00[ASN][1000 genomes]
rs56745684	0.84[ASN][1000 genomes]
rs56868628	0.82[ASN][1000 genomes]
rs58816065	0.84[ASN][1000 genomes]
rs67484139	0.93[ASN][1000 genomes]
rs7025939	0.81[CEU][hapmap]
rs7038256	0.81[CEU][hapmap]
rs72762854	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72762864	0.93[ASN][1000 genomes]
rs739466	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7853626	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7869522	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894114	chr9:136538798-136779153	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv428546	chr9:136541745-136720872	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv831745	chr9:136593702-136780273	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv894117	chr9:136600201-136716399	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv831746	chr9:136607829-136750740	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv894122	chr9:136632662-136760639	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1035272	chr9:136665308-136772256	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	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

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136675200-136728400	Weak transcription	Esophagus	oesophagus
2	chr9:136675400-136709400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:136686000-136709600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr9:136692000-136709800	Weak transcription	NH-A	brain
5	chr9:136697600-136709800	Weak transcription	Primary B cells from cord blood	blood
6	chr9:136698400-136718000	Weak transcription	Hela-S3	cervix
7	chr9:136699000-136709600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:136699200-136708800	Weak transcription	Brain Hippocampus Middle	brain
9	chr9:136700000-136709400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:136700000-136709600	Weak transcription	Gastric	stomach
11	chr9:136700800-136709800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr9:136701000-136707400	Weak transcription	NHEK	skin
13	chr9:136701000-136709800	Weak transcription	Brain Germinal Matrix	brain
14	chr9:136701400-136707600	Weak transcription	Lung	lung
15	chr9:136701400-136708800	Weak transcription	Ovary	ovary
16	chr9:136702000-136707400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:136702000-136708400	Enhancers	Fetal Intestine Large	intestine
18	chr9:136702600-136710000	Weak transcription	GM12878-XiMat	blood
19	chr9:136703200-136708200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:136703600-136706200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr9:136703600-136707000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:136704200-136706800	Enhancers	Placenta	Placenta
23	chr9:136704200-136710200	Enhancers	Fetal Muscle Leg	muscle
24	chr9:136704400-136706200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr9:136704400-136706400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr9:136704600-136708000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:136704800-136706000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:136704800-136706000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr9:136704800-136706000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr9:136704800-136706200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:136704800-136706400	Enhancers	HepG2	liver
32	chr9:136704800-136707200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:136704800-136707800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr9:136704800-136708000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:136704800-136708200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr9:136705000-136706200	Enhancers	Fetal Stomach	stomach
37	chr9:136705000-136706400	Enhancers	Spleen	Spleen
38	chr9:136705000-136707200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:136705000-136707400	Enhancers	Fetal Brain Female	brain
40	chr9:136705000-136707600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:136705000-136709200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:136705200-136706000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:136705200-136706200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:136705200-136707000	Weak transcription	Fetal Thymus	thymus
45	chr9:136705200-136708400	Enhancers	Fetal Brain Male	brain
46	chr9:136705200-136710800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr9:136705200-136710800	Weak transcription	A549	lung
48	chr9:136705200-136711200	Genic enhancers	Fetal Intestine Small	intestine
49	chr9:136705400-136706000	Weak transcription	Pancreas	Pancrea
50	chr9:136705400-136706200	Enhancers	Stomach Smooth Muscle	stomach

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