Variant report

Variant	rs2154053
Chromosome Location	chr10:22937760-22937761
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:22935997..22937858-chr10:22985488..22987779,2	K562	blood:
2	chr10:22935992..22938184-chr10:22964745..22966524,2	MCF-7	breast:
3	chr10:22930057..22932318-chr10:22937347..22939667,3	K562	blood:
4	chr10:22937664..22939892-chr10:22939931..22943485,3	MCF-7	breast:
5	chr10:22936873..22940866-chr10:22947347..22949426,3	K562	blood:
6	chr10:22936873..22939042-chr10:22947347..22949237,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10508649	0.85[JPT][hapmap]
rs10741006	1.00[CHB][hapmap]
rs10828323	0.84[CEU][hapmap]
rs10828324	0.84[CEU][hapmap]
rs10828325	0.80[CEU][hapmap]
rs11013053	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11013066	0.80[CEU][hapmap]
rs11013067	0.80[CEU][hapmap]
rs11013069	0.88[CHB][hapmap]
rs11013077	0.83[CEU][hapmap]
rs11013082	0.88[CEU][hapmap]
rs1171489	0.92[EUR][1000 genomes]
rs1171490	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs1171492	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1171493	0.90[EUR][1000 genomes]
rs1171494	0.87[EUR][1000 genomes]
rs1171497	0.92[CEU][hapmap]
rs1171499	0.94[EUR][1000 genomes]
rs1171502	0.83[ASN][1000 genomes]
rs1171503	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs1171504	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs1171506	0.92[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1171509	0.84[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap]
rs12354766	0.84[CEU][hapmap]
rs12358560	0.80[CEU][hapmap]
rs12774725	0.80[CEU][hapmap]
rs1343504	0.80[CEU][hapmap]
rs1409393	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1409394	0.91[EUR][1000 genomes]
rs1409395	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs1539628	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1614387	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs16922558	0.85[JPT][hapmap]
rs16922574	0.85[JPT][hapmap]
rs16922619	0.85[JPT][hapmap]
rs16922629	0.85[JPT][hapmap]
rs1750747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1750748	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1750775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1750777	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs1750778	0.84[EUR][1000 genomes]
rs1778334	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1778335	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1778338	0.92[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs1778339	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs1778340	0.84[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs1778342	0.92[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778345	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1778346	0.92[EUR][1000 genomes]
rs1778347	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2559534	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2766001	0.85[ASN][1000 genomes]
rs2798981	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs34208652	0.82[EUR][1000 genomes]
rs7914338	0.85[JPT][hapmap]
rs943196	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][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	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
2	nsv831809	chr10:22918101-23069676	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2154053	PIP4K2A	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22915000-22951800	Weak transcription	Fetal Intestine Small	intestine
2	chr10:22921000-22940400	Weak transcription	Ovary	ovary
3	chr10:22926000-22938600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr10:22927800-22942800	Enhancers	Brain Anterior Caudate	brain
5	chr10:22929200-22938600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:22929600-22948400	Enhancers	Brain Cingulate Gyrus	brain
7	chr10:22929800-22939800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:22930400-22938600	Enhancers	Brain Hippocampus Middle	brain
9	chr10:22931200-22938400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr10:22931200-22938400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:22931600-22941000	Enhancers	Brain Angular Gyrus	brain
12	chr10:22932400-22940400	Enhancers	Fetal Thymus	thymus
13	chr10:22932400-22944200	Weak transcription	Brain Germinal Matrix	brain
14	chr10:22933600-22938400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr10:22933600-22944200	Weak transcription	Fetal Stomach	stomach
16	chr10:22934800-22937800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr10:22934800-22939400	Enhancers	Dnd41	blood
18	chr10:22934800-22942400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr10:22935000-22938200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:22935000-22938600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr10:22935000-22939000	Enhancers	Thymus	Thymus
22	chr10:22935000-22945400	Enhancers	Primary B cells from peripheral blood	blood
23	chr10:22935200-22938400	Enhancers	Primary T cells fromperipheralblood	blood
24	chr10:22935200-22938600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr10:22935200-22938600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr10:22935200-22938800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr10:22935200-22939200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr10:22935200-22953000	Enhancers	Brain Substantia Nigra	brain
29	chr10:22935400-22937800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:22935400-22938000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr10:22935400-22938800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr10:22935600-22937800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr10:22935600-22938000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr10:22935600-22938000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr10:22935600-22938800	Enhancers	H1 Cell Line	embryonic stem cell
36	chr10:22935600-22939000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr10:22935800-22938200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr10:22936000-22938000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr10:22936000-22938200	Enhancers	Adipose Nuclei	Adipose
40	chr10:22936000-22938400	Enhancers	Fetal Kidney	kidney
41	chr10:22936200-22938000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:22936200-22938000	Enhancers	Fetal Heart	heart
43	chr10:22936200-22938600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:22936200-22938600	Enhancers	HSMMtube	muscle
45	chr10:22936200-22939600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr10:22936400-22937800	Enhancers	H9 Cell Line	embryonic stem cell
47	chr10:22936400-22937800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr10:22936400-22937800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr10:22936400-22958000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr10:22936600-22937800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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