Variant report

Variant	rs2807978
Chromosome Location	chr10:22208630-22208631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10508639	0.85[CEU][hapmap]
rs10740991	0.80[CEU][hapmap]
rs10740997	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764330	0.80[CEU][hapmap]
rs10828266	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs1086896	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1086899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11012794	0.82[MEX][hapmap]
rs12571634	0.90[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2066270	0.80[CEU][hapmap]
rs2066271	0.80[CEU][hapmap]
rs2252343	0.80[ASN][1000 genomes]
rs2457954	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2487512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2666750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2666753	0.90[CEU][hapmap];0.84[GIH][hapmap]
rs2666754	0.85[EUR][1000 genomes]
rs2666756	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2666757	0.85[EUR][1000 genomes]
rs2666759	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666760	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2666761	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666762	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2666768	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2666769	0.80[CEU][hapmap]
rs2666771	0.85[CEU][hapmap]
rs2666772	0.80[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs2666775	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2666776	0.86[EUR][1000 genomes]
rs2666779	0.80[CEU][hapmap]
rs2666781	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2666782	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs2793341	0.80[ASN][1000 genomes]
rs2793351	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2793352	0.80[ASN][1000 genomes]
rs2807966	0.84[EUR][1000 genomes]
rs2807968	0.85[EUR][1000 genomes]
rs2807971	0.85[CEU][hapmap]
rs2807979	0.85[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2807980	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2807982	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2807983	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2807984	0.85[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs2807985	0.80[CEU][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs2807986	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs2807987	0.85[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs2807988	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2859622	0.84[EUR][1000 genomes]
rs2941732	0.80[EUR][1000 genomes]
rs2941733	0.81[EUR][1000 genomes]
rs2998360	0.80[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4024198	0.85[CEU][hapmap]
rs4146689	0.85[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs4364959	0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs4748776	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4748777	0.81[CEU][hapmap]
rs4748779	0.85[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs6650129	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650130	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072776	1.00[CHB][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs7082663	0.80[CEU][hapmap];0.87[TSI][hapmap]
rs7089656	0.85[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs7898685	1.00[CHB][hapmap]
rs7904395	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7910002	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs792452	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs792453	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs792454	0.86[EUR][1000 genomes]
rs806774	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052464	chr10:21856531-22220087	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv1802317	chr10:21866085-22288132	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1793816	chr10:22088054-22285371	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1048924	chr10:22177164-22296409	Enhancers Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv831808	chr10:22187850-22357814	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv894948	chr10:22203392-22255097	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	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
rs2807978	PIP4K2A	cis	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22179000-22224000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr10:22183400-22221000	Weak transcription	Left Ventricle	heart
3	chr10:22183800-22215600	Weak transcription	HSMM	muscle
4	chr10:22185000-22222000	Weak transcription	Right Ventricle	heart
5	chr10:22185200-22210200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr10:22188600-22214800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr10:22188800-22210000	Weak transcription	Ovary	ovary
8	chr10:22188800-22213800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr10:22188800-22229200	Weak transcription	Aorta	Aorta
10	chr10:22189000-22209000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr10:22189000-22210600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr10:22191000-22215600	Weak transcription	NHDF-Ad	bronchial
13	chr10:22193000-22210400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:22193000-22215000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr10:22193000-22215400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:22193000-22224200	Weak transcription	Primary B cells from cord blood	blood
17	chr10:22193200-22214800	Weak transcription	Placenta	Placenta
18	chr10:22193200-22216800	Weak transcription	Liver	Liver
19	chr10:22193400-22216000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr10:22193400-22216000	Weak transcription	K562	blood
21	chr10:22193600-22209000	Weak transcription	NH-A	brain
22	chr10:22193600-22210400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:22196200-22223400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr10:22196800-22216800	Weak transcription	Fetal Intestine Small	intestine
25	chr10:22199200-22216000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr10:22199600-22250800	Weak transcription	Pancreas	Pancrea
27	chr10:22202000-22215600	Weak transcription	Fetal Lung	lung
28	chr10:22202200-22216000	Weak transcription	GM12878-XiMat	blood
29	chr10:22202800-22210400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr10:22202800-22210600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr10:22203000-22215000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr10:22203000-22221200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:22203400-22215600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr10:22204600-22214800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr10:22204800-22209000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr10:22204800-22209800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr10:22207200-22209600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr10:22207600-22209000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr10:22207600-22209000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr10:22207600-22209000	Enhancers	Fetal Heart	heart
41	chr10:22207600-22209200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr10:22207600-22212200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr10:22208000-22209000	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr10:22208000-22209200	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr10:22208400-22209000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr10:22208400-22215000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr10:22208400-22215000	Weak transcription	Muscle Satellite Cultured Cells	--

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