Variant report

Variant	rs10812488
Chromosome Location	chr9:26891243-26891244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr9:26890977-26893272	Hela-S3	cervix:	n/a	n/a
2	GATA3	chr9:26890860-26891459	SK-N-SH	brain:	n/a	n/a
3	GATA1	chr9:26891072-26893052	PBDE	blood:	n/a	n/a
4	POLR2A	chr9:26891212-26893831	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr9:26890917-26893711	K562	blood:	n/a	n/a
6	TBL1XR1	chr9:26891049-26893676	K562	blood:	n/a	n/a
7	POLR2A	chr9:26891084-26893746	MCF10A-Er-Src	breast:	n/a	n/a
8	GATA3	chr9:26890935-26891334	SK-N-SH	brain:	n/a	n/a
9	MXI1	chr9:26890843-26893800	SK-N-SH	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:26890555..26892142-chr9:26919709..26921210,2	MCF-7	breast:
2	chr9:26891080..26895841-chr9:26945501..26948974,8	K562	blood:
3	chr9:26891080..26894676-chr9:26945695..26949113,9	K562	blood:
4	chr9:26886338..26888156-chr9:26890310..26892766,2	MCF-7	breast:
5	chr9:26890425..26894629-chr9:26953159..26958312,6	K562	blood:
6	chr9:26890972..26893985-chr9:26945405..26948624,3	MCF-7	breast:
7	chr9:26886474..26888568-chr9:26890678..26892880,3	MCF-7	breast:
8	chr9:26890485..26893190-chr9:26945159..26948755,7	MCF-7	breast:
9	chr9:26889862..26894629-chr9:26953159..26958871,9	K562	blood:
10	chr9:26886311..26888299-chr9:26891061..26892871,2	K562	blood:

No data

Variant related genes	Relation type
RN7SL100P	TF binding region
CAAP1	TF binding region
ENSG00000120159	Chromatin interaction
ENSG00000096872	Chromatin interaction
ENSG00000137055	Chromatin interaction
ENSG00000234676	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10738762	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10757634	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10757635	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10757636	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10812479	0.86[EUR][1000 genomes]
rs10812482	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10812487	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10812503	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10812504	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10812507	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs10812518	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs10967548	0.88[EUR][1000 genomes]
rs10967549	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10967551	0.87[EUR][1000 genomes]
rs10967556	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10967645	0.81[CHB][hapmap]
rs10967652	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10967679	0.83[JPT][hapmap]
rs12337896	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs12342005	0.82[CEU][hapmap]
rs12345197	0.83[AFR][1000 genomes]
rs1541144	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1819539	0.81[JPT][hapmap]
rs2225720	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs3758218	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs4316229	0.84[AFR][1000 genomes]
rs4413873	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4621911	0.83[JPT][hapmap]
rs59159685	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6475944	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6475945	0.89[CEU][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6475946	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6475947	0.89[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6475954	0.83[JPT][hapmap]
rs7018585	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs7020010	0.88[CHB][hapmap]
rs7032756	0.82[CEU][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs7033238	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7034478	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7034670	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7035292	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7038218	0.94[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7040505	0.83[CEU][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes]
rs7042133	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7042447	0.89[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7849248	0.87[CHB][hapmap]
rs7856462	0.89[CEU][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7857481	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7857669	0.83[JPT][hapmap]
rs7860542	0.85[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7863476	0.88[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7868158	0.88[CEU][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7870787	0.83[CHB][hapmap]
rs7871668	0.83[JPT][hapmap]
rs7875068	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	nsv1026827	chr9:26693515-26904699	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10812488	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26836600-26891400	Weak transcription	Brain Substantia Nigra	brain
2	chr9:26851800-26891600	Weak transcription	Stomach Mucosa	stomach
3	chr9:26882800-26891400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:26882800-26891600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:26882800-26891800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:26882800-26892000	Weak transcription	Lung	lung
7	chr9:26883000-26891600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:26883000-26891600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:26883000-26891600	Weak transcription	Small Intestine	intestine
10	chr9:26883200-26892200	Weak transcription	Spleen	Spleen
11	chr9:26883400-26891800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:26883400-26892200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:26883600-26891400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr9:26883600-26891600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:26883600-26891600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:26884600-26891600	Weak transcription	Placenta	Placenta
17	chr9:26885800-26891400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:26887600-26891600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr9:26888000-26891400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr9:26888200-26891400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr9:26888200-26893600	Active TSS	K562	blood
22	chr9:26888400-26891600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr9:26888400-26891600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr9:26889000-26891400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:26889200-26891600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:26889400-26891400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr9:26889600-26891400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:26889600-26891400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr9:26889600-26891800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:26890000-26891400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:26890000-26891400	Enhancers	Colon Smooth Muscle	Colon
32	chr9:26890000-26893000	Active TSS	Hela-S3	cervix
33	chr9:26890200-26891400	Enhancers	Fetal Brain Male	brain
34	chr9:26890200-26893400	Active TSS	Psoas Muscle	Psoas
35	chr9:26890200-26893600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr9:26890400-26891600	Enhancers	Primary B cells from cord blood	blood
37	chr9:26890400-26891600	Weak transcription	Left Ventricle	heart
38	chr9:26890400-26894400	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr9:26890600-26891400	Active TSS	HepG2	liver
40	chr9:26890600-26891600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr9:26890600-26892000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:26890600-26893000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:26890600-26893200	Active TSS	Fetal Intestine Large	intestine
44	chr9:26890600-26893200	Active TSS	A549	lung
45	chr9:26890600-26893600	Active TSS	Fetal Intestine Small	intestine
46	chr9:26890600-26893600	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr9:26890800-26891400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:26890800-26891400	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr9:26890800-26891600	Enhancers	Brain Hippocampus Middle	brain
50	chr9:26890800-26891600	Weak transcription	Ovary	ovary

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