Variant report

Variant	rs12249889
Chromosome Location	chr10:25314538-25314539
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:25304238..25308721-chr10:25308828..25316334,14	MCF-7	breast:
2	chr10:25011848..25014443-chr10:25313188..25315931,2	K562	blood:
3	chr10:25309325..25311704-chr10:25312754..25314813,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185875	Chromatin interaction
ENSG00000107863	Chromatin interaction
ENSG00000151023	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1000875	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508685	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs10508686	0.91[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10764515	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[ASN][1000 genomes]
rs10764516	0.97[ASN][1000 genomes]
rs10764517	0.99[ASN][1000 genomes]
rs10764518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764519	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap]
rs10828740	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828743	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10828744	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828745	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs10828747	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11014347	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014348	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11014351	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11014357	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs11014360	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11014361	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11014362	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11014365	0.83[CHB][hapmap];0.93[GIH][hapmap]
rs1124017	0.99[ASN][1000 genomes]
rs11593926	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598879	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12219239	0.81[CHB][hapmap]
rs12256642	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356765	0.99[ASN][1000 genomes]
rs12761282	0.81[ASN][1000 genomes]
rs12769388	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12776058	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12781953	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12784769	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs1352982	0.85[ASN][1000 genomes]
rs1352984	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1352985	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492608	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546097	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];1.00[ASN][1000 genomes]
rs1907791	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2031600	0.80[ASN][1000 genomes]
rs2087782	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131275	0.81[AMR][1000 genomes]
rs2131276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131277	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220707	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279547	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs2291583	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291584	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291585	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291586	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307047	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs2367506	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274290	0.80[ASN][1000 genomes]
rs274301	0.95[CHB][hapmap]
rs274305	0.81[CHB][hapmap]
rs274311	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs274313	0.81[CHB][hapmap]
rs4345864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4747509	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4747510	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4747511	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4748993	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs4748994	0.89[ASN][1000 genomes]
rs4748996	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748997	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748998	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748999	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4749000	0.83[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4749001	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56192563	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60251099	0.84[ASN][1000 genomes]
rs6482467	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs6482468	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs7082131	0.98[ASN][1000 genomes]
rs7086282	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs7095364	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7393543	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs7913853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902903	0.81[ASN][1000 genomes]
rs902904	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902906	0.93[GIH][hapmap]
rs950609	0.99[ASN][1000 genomes]
rs987274	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12249889	PIP4K2A	cis	parietal	SCAN
rs12249889	THNSL1	cis	parietal	SCAN
rs12249889	THNSL1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25306600-25315400	Weak transcription	NHDF-Ad	bronchial
2	chr10:25306600-25316400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr10:25307000-25316400	Weak transcription	Brain Germinal Matrix	brain
4	chr10:25307000-25316800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr10:25307000-25317000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:25307000-25317000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:25307000-25325400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr10:25307200-25314800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:25307400-25315800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr10:25307400-25316200	Weak transcription	Fetal Lung	lung
11	chr10:25307600-25316400	Weak transcription	Primary B cells from cord blood	blood
12	chr10:25308000-25314600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr10:25308800-25314600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr10:25312600-25315200	Strong transcription	Primary T cells from cord blood	blood
15	chr10:25312600-25316000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:25312800-25314800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:25312800-25316600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr10:25313000-25315200	Weak transcription	Brain Angular Gyrus	brain
19	chr10:25313200-25315200	Weak transcription	Ovary	ovary
20	chr10:25313400-25315200	Weak transcription	Brain Anterior Caudate	brain
21	chr10:25313400-25315200	Weak transcription	Brain Substantia Nigra	brain
22	chr10:25313800-25317200	Weak transcription	Osteobl	bone
23	chr10:25314200-25315200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:25314200-25315400	Enhancers	Liver	Liver
25	chr10:25314200-25317200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr10:25314400-25317200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr10:25314400-25317600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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