Variant report

Variant	rs12417769
Chromosome Location	chr11:66437010-66437011
allele	C/T
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	chr11:66437006-66438462	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr11:66432551-66437019	U87	brain:	n/a	n/a
3	POLR2A	chr11:66436972-66439009	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr11:66432453-66439184	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr11:66432929-66437013	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66433561..66435825-chr11:66436517..66438156,2	MCF-7	breast:
2	chr11:66412064..66414929-chr11:66436700..66439361,2	K562	blood:
3	chr11:66434858..66442780-chr11:66443506..66446731,13	MCF-7	breast:

Variant related genes	Relation type
RBM4B	TF binding region
ENSG00000173914	Chromatin interaction
ENSG00000258297	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12577111	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12804382	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12805133	0.94[ASN][1000 genomes]
rs2276138	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34900764	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3741363	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474602	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs477557	0.86[ASN][1000 genomes]
rs4930387	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs508443	0.86[ASN][1000 genomes]
rs535211	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs577023	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs577335	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs580910	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6591221	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv518919	chr11:66409409-66468469	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12417769	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs12417769	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs12417769	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66411800-66442800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:66412000-66438800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:66413000-66440400	Strong transcription	Fetal Stomach	stomach
4	chr11:66413000-66442600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:66413400-66438400	Strong transcription	Dnd41	blood
6	chr11:66413600-66438400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:66414800-66442600	Weak transcription	Small Intestine	intestine
8	chr11:66415000-66438800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr11:66420000-66438400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:66420600-66443800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:66422200-66439400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:66422800-66438600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:66424000-66438800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:66424200-66438400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:66424200-66438600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:66424200-66439200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:66424400-66438800	Strong transcription	Fetal Intestine Large	intestine
18	chr11:66426000-66439200	Strong transcription	Primary T cells from cord blood	blood
19	chr11:66426800-66438800	Strong transcription	HSMM	muscle
20	chr11:66427600-66443200	Weak transcription	Stomach Mucosa	stomach
21	chr11:66428000-66438800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:66428000-66438800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:66428400-66438600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr11:66428400-66438600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:66428400-66438600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:66428400-66438800	Strong transcription	Hela-S3	cervix
27	chr11:66428600-66438400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:66429400-66438000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr11:66430600-66438400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:66430800-66438800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:66432000-66437800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr11:66432000-66437800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr11:66432000-66438200	Strong transcription	Placenta	Placenta
34	chr11:66432000-66438600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr11:66432200-66438000	Strong transcription	Osteobl	bone
36	chr11:66432200-66438400	Strong transcription	K562	blood
37	chr11:66432200-66438800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:66432400-66437600	Strong transcription	Liver	Liver
39	chr11:66432400-66438400	Strong transcription	A549	lung
40	chr11:66432600-66438000	Strong transcription	Fetal Kidney	kidney
41	chr11:66432800-66437600	Strong transcription	HepG2	liver
42	chr11:66433000-66437800	Weak transcription	Psoas Muscle	Psoas
43	chr11:66433400-66438000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:66433400-66438800	Strong transcription	Primary B cells from cord blood	blood
45	chr11:66433600-66437800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:66433600-66438200	Weak transcription	Fetal Heart	heart
47	chr11:66434000-66443800	Weak transcription	Colonic Mucosa	Colon
48	chr11:66434000-66444600	Weak transcription	Aorta	Aorta
49	chr11:66434400-66439400	Genic enhancers	Fetal Thymus	thymus
50	chr11:66434800-66442800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links