Variant report

Variant	rs2559528
Chromosome Location	chr10:22899041-22899042
allele	C/G/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	CTCF	chr10:22898920-22899070	BE2_C	brain:	n/a	n/a
2	CUX1	chr10:22899040-22899067	GM12878	blood:	n/a	n/a
3	RAD21	chr10:22898668-22899152	MCF-7	breast:	n/a	chr10:22898857-22898876
4	RAD21	chr10:22898633-22899146	MCF-7	breast:	n/a	chr10:22898857-22898876

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:22898960..22901520-chr10:22921454..22923581,2	K562	blood:

Variant related genes	Relation type
PIP4K2A	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11013054	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1171505	0.87[CHB][hapmap]
rs1326341	0.80[YRI][hapmap]
rs1409397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1409398	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1750750	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1750754	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1750755	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1750756	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1750757	0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1750758	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1778303	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs1778304	0.89[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1778316	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1778331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1778351	0.84[JPT][hapmap]
rs1778353	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1778355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1778356	0.86[JPT][hapmap];0.95[YRI][hapmap]
rs2256542	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2364116	0.85[ASN][1000 genomes]
rs2559522	0.86[JPT][hapmap]
rs2559523	0.86[JPT][hapmap];0.82[AFR][1000 genomes]
rs2559524	0.84[JPT][hapmap]
rs2559526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2559527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2765994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2765995	0.86[JPT][hapmap]
rs2765998	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2798982	0.86[JPT][hapmap];0.96[YRI][hapmap]
rs2913109	0.86[JPT][hapmap]
rs2913110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7071450	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7098460	0.86[JPT][hapmap]
rs7099314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs754822	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7912144	0.86[JPT][hapmap]
rs943194	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs943195	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][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	esv1830947	chr10:22881196-23004381	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22844200-22904800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:22856600-22899200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:22858200-22904000	Weak transcription	Colonic Mucosa	Colon
4	chr10:22862400-22902000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:22880000-22906800	Weak transcription	Colon Smooth Muscle	Colon
6	chr10:22883200-22899200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr10:22887200-22902400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr10:22888800-22905000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:22889400-22904400	Weak transcription	Hela-S3	cervix
10	chr10:22891000-22901400	Weak transcription	Gastric	stomach
11	chr10:22891000-22904800	Weak transcription	Right Ventricle	heart
12	chr10:22891200-22904800	Weak transcription	NHLF	lung
13	chr10:22893600-22902000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr10:22894000-22902600	Weak transcription	Right Atrium	heart
15	chr10:22894000-22906600	Weak transcription	Ovary	ovary
16	chr10:22894200-22904600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr10:22894600-22903000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr10:22894600-22904400	Weak transcription	NHDF-Ad	bronchial
19	chr10:22894600-22904600	Weak transcription	NHEK	skin
20	chr10:22894600-22905000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr10:22894800-22899400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr10:22894800-22904600	Weak transcription	Adipose Nuclei	Adipose
23	chr10:22894800-22913000	Weak transcription	Fetal Kidney	kidney
24	chr10:22895200-22899200	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr10:22895400-22899400	Genic enhancers	Brain Hippocampus Middle	brain
26	chr10:22895400-22904600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr10:22895600-22899400	Weak transcription	HepG2	liver
28	chr10:22895600-22901000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr10:22895600-22902000	Weak transcription	Pancreas	Pancrea
30	chr10:22895600-22902200	Weak transcription	Placenta	Placenta
31	chr10:22895600-22906000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:22895800-22900200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:22895800-22904600	Weak transcription	HUVEC	blood vessel
34	chr10:22895800-22904800	Weak transcription	NH-A	brain
35	chr10:22896000-22899800	Strong transcription	K562	blood
36	chr10:22896000-22902600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr10:22896200-22899600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr10:22896200-22901600	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr10:22896400-22904000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr10:22896400-22904600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr10:22896400-22904600	Weak transcription	A549	lung
42	chr10:22896400-22904800	Weak transcription	Osteobl	bone
43	chr10:22896600-22899400	Genic enhancers	GM12878-XiMat	blood
44	chr10:22896600-22899600	Strong transcription	Dnd41	blood
45	chr10:22896600-22902200	Weak transcription	Esophagus	oesophagus
46	chr10:22896600-22904600	Weak transcription	HSMM	muscle
47	chr10:22896800-22899400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr10:22897000-22899200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr10:22897200-22899400	Weak transcription	Brain Angular Gyrus	brain
50	chr10:22897200-22900400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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