Variant report

Variant	rs12683896
Chromosome Location	chr9:97689690-97689691
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97687410..97690571-chr9:97710837..97713862,3	MCF-7	breast:
2	chr17:58662561..58665410-chr9:97687576..97689964,2	MCF-7	breast:
3	chr9:97687308..97690068-chr9:97855270..97858001,3	MCF-7	breast:
4	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
5	chr9:97688111..97690470-chr9:97723342..97725072,2	MCF-7	breast:
6	chr9:97685017..97689714-chr9:97737820..97743340,6	MCF-7	breast:
7	chr9:97688794..97691032-chr9:97848721..97850468,2	MCF-7	breast:
8	chr9:97572097..97590438-chr9:97672990..97690806,63	MCF-7	breast:
9	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
10	chr9:97687078..97690879-chr9:97725543..97729239,3	MCF-7	breast:
11	chr9:97688725..97690345-chr9:97748989..97750908,2	MCF-7	breast:
12	chr9:97688635..97691116-chr9:97722109..97725030,2	MCF-7	breast:
13	chr9:97688920..97691846-chr9:97741162..97743776,2	K562	blood:
14	chr9:97393231..97394953-chr9:97687496..97690303,2	MCF-7	breast:
15	chr9:97559408..97562110-chr9:97687505..97689946,2	MCF-7	breast:
16	chr9:97562492..97588737-chr9:97670126..97691056,102	MCF-7	breast:
17	chr9:97627475..97632236-chr9:97687625..97689828,4	MCF-7	breast:
18	chr9:97687964..97690417-chr9:97736353..97738694,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000230815	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000252153	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10125566	0.84[AMR][1000 genomes]
rs10217441	0.84[AMR][1000 genomes]
rs10732407	0.84[AMR][1000 genomes]
rs10739988	0.84[AMR][1000 genomes]
rs10739990	0.84[AMR][1000 genomes]
rs10761362	0.81[AMR][1000 genomes]
rs10821411	0.84[AMR][1000 genomes]
rs1113967	0.84[AMR][1000 genomes]
rs12551506	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552838	1.00[AMR][1000 genomes]
rs12554043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1382411	0.88[AMR][1000 genomes]
rs1382412	0.88[AMR][1000 genomes]
rs1542107	0.84[AMR][1000 genomes]
rs16911834	1.00[AMR][1000 genomes]
rs16911856	0.80[AMR][1000 genomes]
rs1904201	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026399	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095069	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119953	0.84[AMR][1000 genomes]
rs2406897	0.84[AMR][1000 genomes]
rs2406898	0.84[AMR][1000 genomes]
rs2897523	0.84[AMR][1000 genomes]
rs3847311	0.81[AMR][1000 genomes]
rs3886568	0.84[AMR][1000 genomes]
rs41316526	0.88[AMR][1000 genomes]
rs4332191	0.84[AMR][1000 genomes]
rs4744389	0.84[AMR][1000 genomes]
rs6479581	0.84[AMR][1000 genomes]
rs66642068	0.88[AMR][1000 genomes]
rs66863985	0.88[AMR][1000 genomes]
rs66993340	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67490803	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67756624	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019602	0.84[AMR][1000 genomes]
rs7029570	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7044371	0.84[AMR][1000 genomes]
rs7046900	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72748601	1.00[AMR][1000 genomes]
rs72750306	0.82[AFR][1000 genomes]
rs73538177	0.88[AMR][1000 genomes]
rs7869736	0.84[AMR][1000 genomes]
rs894426	0.84[AMR][1000 genomes]
rs894427	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:97680400-97698000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:97680600-97700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:97682000-97713800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:97682200-97691200	Enhancers	Placenta	Placenta
7	chr9:97684200-97699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:97684800-97690000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:97684800-97711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:97685000-97690400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:97685200-97690600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:97685200-97693000	Weak transcription	Small Intestine	intestine
13	chr9:97685200-97714600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:97685400-97690200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr9:97685400-97690600	Weak transcription	HUVEC	blood vessel
16	chr9:97685600-97690200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:97685600-97699600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:97685800-97689800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:97685800-97690000	Weak transcription	Right Ventricle	heart
20	chr9:97685800-97690400	Weak transcription	Fetal Lung	lung
21	chr9:97685800-97693600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:97686000-97690400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:97686000-97690800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:97686000-97691400	Weak transcription	Spleen	Spleen
25	chr9:97686000-97698800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:97686200-97689800	Weak transcription	NH-A	brain
27	chr9:97686200-97690000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:97686200-97690200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:97686200-97690400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:97686200-97690800	Strong transcription	Primary T cells from cord blood	blood
31	chr9:97686200-97694200	Genic enhancers	A549	lung
32	chr9:97686400-97690000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:97686400-97690000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr9:97686400-97690200	Weak transcription	Brain Substantia Nigra	brain
35	chr9:97686400-97690400	Weak transcription	Brain Angular Gyrus	brain
36	chr9:97686400-97691600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr9:97686400-97695200	Weak transcription	Ovary	ovary
38	chr9:97686600-97689800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:97686600-97690000	Weak transcription	Brain Anterior Caudate	brain
40	chr9:97686600-97690200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:97686600-97690200	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:97686600-97690600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:97686600-97691200	Weak transcription	Right Atrium	heart
44	chr9:97686800-97689800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:97686800-97689800	Weak transcription	NHLF	lung
46	chr9:97686800-97690000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:97686800-97690200	Strong transcription	Osteobl	bone
48	chr9:97686800-97691800	Weak transcription	Brain Germinal Matrix	brain
49	chr9:97687000-97693800	Enhancers	HepG2	liver
50	chr9:97687000-97699400	Weak transcription	Fetal Heart	heart

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