Variant report

Variant	rs1039966
Chromosome Location	chr10:23656316-23656317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:23656227..23658764-chr10:23659457..23661559,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10159586	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10159622	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10159725	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10734044	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10734045	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10764400	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10828434	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11013381	0.82[CHD][hapmap]
rs11013409	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2036917	0.92[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2036918	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2036919	1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2036920	1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2036921	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2137156	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2175503	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4075675	0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4326695	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4575157	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4747464	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4747465	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4748864	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4748865	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4748867	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4748868	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4748869	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4748870	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4748872	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4748873	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6482267	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6482268	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6482269	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7076538	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7085049	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7087803	0.84[EUR][1000 genomes]
rs7092292	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7893984	0.84[EUR][1000 genomes]
rs7894108	0.85[EUR][1000 genomes]
rs7894725	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7898413	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7906070	0.81[CEU][hapmap]
rs7913858	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7923763	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs869158	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9299781	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9299782	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1039966	PRTFDC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:23650600-23657600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr10:23653200-23657200	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr10:23653800-23656800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:23653800-23657200	Weak transcription	Fetal Thymus	thymus
5	chr10:23653800-23657600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr10:23654200-23656400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr10:23654400-23657200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:23654800-23656400	Weak transcription	GM12878-XiMat	blood
9	chr10:23654800-23657400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:23655000-23656400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:23655000-23656800	Weak transcription	NHEK	skin
12	chr10:23655000-23659400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr10:23655200-23656800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr10:23655400-23656800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr10:23655400-23657000	Weak transcription	HMEC	breast
16	chr10:23655600-23657000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr10:23655600-23657200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:23655600-23657600	Enhancers	Primary B cells from peripheral blood	blood
19	chr10:23655600-23659600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr10:23655800-23656800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:23655800-23658400	Weak transcription	Left Ventricle	heart
22	chr10:23656000-23657200	Enhancers	Dnd41	blood
23	chr10:23656000-23657400	Enhancers	Primary B cells from cord blood	blood
24	chr10:23656200-23657200	Enhancers	Primary T cells from cord blood	blood
25	chr10:23656200-23657200	Weak transcription	Stomach Mucosa	stomach
26	chr10:23656200-23658600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr10:23656200-23659400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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