Variant report

Variant	rs2487512
Chromosome Location	chr10:22137880-22137881
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10508639	0.85[CEU][hapmap]
rs10740991	0.80[CEU][hapmap]
rs10740997	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs10764330	0.80[CEU][hapmap]
rs10828266	0.80[CEU][hapmap]
rs10828283	0.80[EUR][1000 genomes]
rs1086896	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1086897	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1086899	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11816415	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12571634	0.90[CEU][hapmap]
rs2066270	0.80[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2066271	0.80[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2252343	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2457954	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2666753	0.90[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2666756	0.90[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2666759	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2666760	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2666761	0.86[ASN][1000 genomes]
rs2666762	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2666763	0.85[AMR][1000 genomes]
rs2666768	0.85[CEU][hapmap]
rs2666769	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs2666771	0.85[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2666772	0.80[CEU][hapmap]
rs2666775	0.85[CEU][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2666779	0.80[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2666781	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2666782	0.85[CEU][hapmap]
rs2793341	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2793351	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2793352	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2807971	0.85[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs2807978	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]
rs2807979	0.85[CEU][hapmap]
rs2807980	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2807982	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2807983	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2807984	0.85[CEU][hapmap]
rs2807985	0.80[CEU][hapmap]
rs2807986	0.80[CEU][hapmap]
rs2807987	0.85[CEU][hapmap]
rs2807988	0.95[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2998360	0.80[CEU][hapmap]
rs4024198	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs4146689	0.85[CEU][hapmap]
rs4748777	0.81[CEU][hapmap]
rs4748779	0.85[CEU][hapmap]
rs6650129	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs6650130	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7072776	1.00[CHB][hapmap]
rs7082663	0.80[CEU][hapmap]
rs7089656	0.85[CEU][hapmap]
rs7898685	1.00[CHB][hapmap]
rs7904395	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910002	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs792452	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs792453	0.80[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs792455	0.88[EUR][1000 genomes]
rs792456	0.83[EUR][1000 genomes]
rs792457	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs792458	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs806772	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs806774	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2487512	PIP4K2A	cis	lymphoblastoid	seeQTL
rs2487512	MLLT10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22121600-22138400	Weak transcription	Primary B cells from cord blood	blood
2	chr10:22123200-22138600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr10:22124200-22169800	Weak transcription	Right Ventricle	heart
4	chr10:22124400-22163000	Weak transcription	Ovary	ovary
5	chr10:22126200-22138200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr10:22126200-22138400	Weak transcription	Adipose Nuclei	Adipose
7	chr10:22126200-22138600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:22126200-22138600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr10:22126200-22161800	Weak transcription	Left Ventricle	heart
10	chr10:22126400-22138400	Weak transcription	Liver	Liver
11	chr10:22126600-22151000	Weak transcription	Fetal Stomach	stomach
12	chr10:22126600-22161800	Weak transcription	Pancreas	Pancrea
13	chr10:22133000-22157800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr10:22133400-22161000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr10:22134000-22138000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr10:22134200-22138000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr10:22134600-22140600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr10:22136000-22138200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:22136400-22142200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:22136600-22138400	Weak transcription	Fetal Lung	lung
21	chr10:22136800-22138000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:22137600-22138800	ZNF genes & repeats	Primary T cells from cord blood	blood
23	chr10:22137600-22159400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr10:22137800-22140600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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