Variant report

Variant	rs1086899
Chromosome Location	chr10:22141442-22141443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10508639	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs10740991	0.80[CEU][hapmap]
rs10740997	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10764330	0.80[CEU][hapmap]
rs10828266	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs1086896	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1086897	0.82[AMR][1000 genomes]
rs11012794	0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs11816415	0.81[AMR][1000 genomes]
rs12571634	0.90[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2066270	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs2066271	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs2252343	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2457954	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2487512	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]
rs2666750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs2666753	0.90[CEU][hapmap]
rs2666756	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2666759	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2666760	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2666761	0.93[ASN][1000 genomes]
rs2666763	0.81[AMR][1000 genomes]
rs2666768	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2666769	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs2666771	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2666772	0.80[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs2666775	0.85[CEU][hapmap]
rs2666776	0.81[EUR][1000 genomes]
rs2666779	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs2666781	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs2666782	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs2793341	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2793351	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2793352	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2807971	0.85[CEU][hapmap]
rs2807978	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]
rs2807979	0.85[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2807980	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2807982	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2807983	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2807984	0.85[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2807985	0.80[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs2807986	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs2807987	0.85[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs2807988	0.95[CEU][hapmap];0.84[AMR][1000 genomes]
rs2998360	0.80[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4024198	0.85[CEU][hapmap]
rs4146689	0.85[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs4364959	0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs4748776	0.82[TSI][hapmap]
rs4748777	0.81[CEU][hapmap]
rs4748779	0.85[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs6650129	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6650130	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7072776	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs7082663	0.80[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs7089656	0.85[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs7898685	1.00[CHB][hapmap]
rs7904395	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7910002	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs792452	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs792453	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs792454	0.88[EUR][1000 genomes]
rs792457	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs792458	0.82[EUR][1000 genomes]
rs806772	0.84[EUR][1000 genomes]
rs806774	0.80[CEU][hapmap];0.83[EUR][1000 genomes]

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
rs1086899	PIP4K2A	cis	lymphoblastoid	seeQTL
rs1086899	MLLT10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22124200-22169800	Weak transcription	Right Ventricle	heart
2	chr10:22124400-22163000	Weak transcription	Ovary	ovary
3	chr10:22126200-22161800	Weak transcription	Left Ventricle	heart
4	chr10:22126600-22151000	Weak transcription	Fetal Stomach	stomach
5	chr10:22126600-22161800	Weak transcription	Pancreas	Pancrea
6	chr10:22133000-22157800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr10:22133400-22161000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:22136400-22142200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:22137600-22159400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:22138000-22161400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:22139000-22161200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr10:22139200-22161200	Weak transcription	Fetal Lung	lung
13	chr10:22139600-22149800	Weak transcription	NHEK	skin
14	chr10:22139800-22149800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr10:22140000-22159800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr10:22140600-22144000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr10:22140600-22149800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:22140600-22159400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr10:22140600-22159600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr10:22140800-22146400	Weak transcription	Adipose Nuclei	Adipose
21	chr10:22140800-22156400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:22140800-22169800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr10:22140800-22174800	Weak transcription	HSMM	muscle
24	chr10:22141000-22142200	Weak transcription	Liver	Liver
25	chr10:22141200-22141600	ZNF genes & repeats	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links