Variant report

Variant	rs1288938
Chromosome Location	chr1:226852155-226852156
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	chr1:226849570-226852709	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226828494..226832604-chr1:226851440..226853779,3	K562	blood:
2	chr1:226848680..226852398-chr1:226863556..226867477,3	MCF-7	breast:
3	chr1:226850865..226853471-chr1:226885650..226887593,2	MCF-7	breast:

Variant related genes	Relation type
ITPKB-IT1	TF binding region
ITPKB-AS1	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1070361	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1071530	0.87[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1288936	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1288939	0.93[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768393	0.83[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.97[ASN][1000 genomes]
rs3768396	0.93[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820640	0.87[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs697847	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs708766	0.87[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][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	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226836800-226856200	Enhancers	Left Ventricle	heart
2	chr1:226837400-226856200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:226837400-226856600	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr1:226837400-226856600	Enhancers	Brain Substantia Nigra	brain
5	chr1:226839400-226856200	Enhancers	Fetal Muscle Leg	muscle
6	chr1:226840600-226852600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:226840600-226852800	Enhancers	Primary hematopoietic stem cells	blood
8	chr1:226841800-226856200	Enhancers	Brain Angular Gyrus	brain
9	chr1:226841800-226860600	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:226842200-226852400	Enhancers	Esophagus	oesophagus
11	chr1:226843800-226854400	Enhancers	Brain Hippocampus Middle	brain
12	chr1:226844800-226852400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:226845600-226855600	Enhancers	Placenta	Placenta
14	chr1:226846000-226852200	Enhancers	Right Ventricle	heart
15	chr1:226846000-226852200	Genic enhancers	Thymus	Thymus
16	chr1:226846200-226853000	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr1:226846200-226862400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:226846600-226852200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:226846800-226853000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:226846800-226853000	Enhancers	Colonic Mucosa	Colon
21	chr1:226846800-226854000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:226847000-226852800	Enhancers	Fetal Lung	lung
23	chr1:226847000-226853000	Enhancers	Spleen	Spleen
24	chr1:226847200-226856200	Enhancers	Fetal Muscle Trunk	muscle
25	chr1:226847600-226853000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:226847600-226853200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:226847800-226853200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:226848000-226852600	Enhancers	Fetal Intestine Large	intestine
29	chr1:226848000-226853600	Enhancers	HUVEC	blood vessel
30	chr1:226848200-226852800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:226848200-226853200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:226848400-226853200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr1:226848400-226853600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:226848600-226854800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:226848800-226853000	Enhancers	Stomach Mucosa	stomach
36	chr1:226849000-226853200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr1:226849000-226853400	Enhancers	HSMMtube	muscle
38	chr1:226849200-226852800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr1:226849200-226853400	Weak transcription	Dnd41	blood
40	chr1:226849200-226854600	Enhancers	Colon Smooth Muscle	Colon
41	chr1:226849200-226856200	Enhancers	Right Atrium	heart
42	chr1:226849400-226857200	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr1:226849600-226858400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:226849800-226852200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:226849800-226852200	Enhancers	Fetal Intestine Small	intestine
46	chr1:226849800-226854200	Enhancers	Fetal Stomach	stomach
47	chr1:226850000-226852200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:226850000-226855200	Weak transcription	Fetal Brain Male	brain
49	chr1:226850400-226859400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr1:226850600-226852200	Enhancers	Primary T cells from cord blood	blood

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