Variant report

Variant	rs12001845
Chromosome Location	chr9:26944018-26944019
allele	A/C
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	POLR2A	chr9:26943983-26944091	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:26882668..26884290-chr9:26943587..26946347,2	MCF-7	breast:
2	chr9:26943098..26949574-chr9:26949927..26957421,13	K562	blood:

Variant related genes	Relation type
IFT74	TF binding region
ENSG00000096872	Chromatin interaction
ENSG00000234676	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10283643	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1048949	1.00[ASN][1000 genomes]
rs10511793	1.00[CHB][hapmap]
rs10812492	1.00[CHB][hapmap]
rs10812500	1.00[CHB][hapmap]
rs10967593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10967594	1.00[CHB][hapmap]
rs10967595	1.00[ASN][1000 genomes]
rs10967624	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs10967625	1.00[CHB][hapmap]
rs10967634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10967638	0.82[ASN][1000 genomes]
rs10967639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10967640	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10967644	0.82[ASN][1000 genomes]
rs1161603	1.00[CHB][hapmap]
rs11788136	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11999015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12002068	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12003612	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12338678	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12338827	1.00[ASN][1000 genomes]
rs12339063	0.94[ASN][1000 genomes]
rs12339162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12340500	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12342005	1.00[CHB][hapmap]
rs12343345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12345094	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12349359	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12352441	1.00[CHB][hapmap]
rs12352603	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12352631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12554485	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13293051	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16910832	0.88[ASN][1000 genomes]
rs16910834	0.88[ASN][1000 genomes]
rs16910888	1.00[CHB][hapmap]
rs16910895	1.00[CHB][hapmap]
rs16911083	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17694121	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17694140	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17694300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17694306	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17694549	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17694796	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17755887	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17755911	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17756221	1.00[JPT][hapmap]
rs17756599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2027124	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2152063	1.00[CHB][hapmap]
rs2991949	1.00[CHB][hapmap]
rs3429	1.00[CHB][hapmap]
rs41271173	1.00[ASN][1000 genomes]
rs41272237	0.82[ASN][1000 genomes]
rs41272239	0.82[ASN][1000 genomes]
rs55902149	0.82[ASN][1000 genomes]
rs59478807	0.94[ASN][1000 genomes]
rs596427	1.00[CHB][hapmap]
rs59757728	0.94[ASN][1000 genomes]
rs61331313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615532	1.00[CHB][hapmap]
rs6475948	1.00[CHB][hapmap]
rs6475959	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6475963	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6475966	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6475968	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7037860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7039400	1.00[CHB][hapmap]
rs7040516	1.00[CHB][hapmap]
rs7040772	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7042003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7042119	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7044842	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73433963	1.00[ASN][1000 genomes]
rs73643117	0.94[ASN][1000 genomes]
rs73643119	0.94[ASN][1000 genomes]
rs73643120	0.94[ASN][1000 genomes]
rs73643125	0.82[ASN][1000 genomes]
rs7847280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7871097	1.00[CHB][hapmap]
rs7871286	1.00[CHB][hapmap]
rs7873019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7873161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7873329	1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS 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	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26916800-26945200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:26925800-26945200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:26926000-26945200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:26926000-26945200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:26926000-26945400	Weak transcription	HSMMtube	muscle
6	chr9:26926600-26944200	Weak transcription	NHEK	skin
7	chr9:26926600-26945600	Weak transcription	Fetal Kidney	kidney
8	chr9:26927400-26945600	Weak transcription	Fetal Thymus	thymus
9	chr9:26927800-26945600	Weak transcription	Colonic Mucosa	Colon
10	chr9:26928400-26945200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr9:26928400-26945400	Weak transcription	NH-A	brain
12	chr9:26928600-26945000	Weak transcription	Osteobl	bone
13	chr9:26928600-26945600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:26928800-26944400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:26928800-26944600	Weak transcription	HMEC	breast
16	chr9:26932400-26945400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:26935200-26945400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr9:26936400-26945400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:26936600-26944200	Weak transcription	Liver	Liver
20	chr9:26936800-26944600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:26936800-26945200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:26936800-26945200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:26936800-26945400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:26936800-26945600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:26936800-26945600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:26936800-26945600	Weak transcription	Aorta	Aorta
27	chr9:26937200-26945200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:26938200-26944600	Weak transcription	Brain Anterior Caudate	brain
29	chr9:26938400-26945200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:26938400-26945200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:26938400-26945400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:26938400-26945400	Weak transcription	Fetal Lung	lung
33	chr9:26938400-26945600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:26938600-26945400	Weak transcription	Fetal Intestine Small	intestine
35	chr9:26938600-26945600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:26938600-26945600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr9:26938600-26945600	Weak transcription	Fetal Stomach	stomach
38	chr9:26938800-26944600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:26938800-26945400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr9:26939200-26945200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:26939200-26945600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr9:26939600-26945200	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr9:26939600-26945600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr9:26939600-26945600	Weak transcription	Fetal Intestine Large	intestine
45	chr9:26939800-26945200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:26940000-26948400	Active TSS	GM12878-XiMat	blood
47	chr9:26940200-26944600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr9:26940200-26945200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr9:26940200-26945600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr9:26940400-26945200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links