Variant report

Variant	rs1050565
Chromosome Location	chr17:28576076-28576077
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	chr17:28574725..28577135-chr17:28599053..28600726,2	K562	blood:

Variant related genes	Relation type
ENSG00000108578	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11656408	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11867581	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs11870192	0.86[AMR][1000 genomes]
rs12938714	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12939390	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12941223	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12945042	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12947654	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12949747	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13341611	0.94[JPT][hapmap]
rs1487971	0.84[CEU][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs17767256	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3103303	0.81[ASN][1000 genomes]
rs3110452	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.81[ASN][1000 genomes]
rs33980254	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34353378	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34622227	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35724800	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36000555	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36048853	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3764449	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794806	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816828	0.94[JPT][hapmap]
rs6505165	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs6505169	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs6505173	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs7208052	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7210085	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs7214014	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs7214248	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7214991	0.84[CEU][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs7215330	0.84[CEU][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs7223821	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73268099	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7342921	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7342929	0.94[JPT][hapmap]
rs8072345	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs8078900	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8080149	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1050565	CPD	cis	parietal	SCAN
rs1050565	GOSR1	cis	parietal	SCAN
rs1050565	BLMH	Cis_1M	lymphoblastoid	RTeQTL
rs1050565	ENSG00000108578	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:28566600-28618000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:28567600-28598000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr17:28570400-28611600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:28570800-28596400	Weak transcription	Fetal Brain Male	brain
5	chr17:28571400-28618000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr17:28572200-28607000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:28572400-28583800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:28572400-28585600	Weak transcription	Right Ventricle	heart
9	chr17:28572400-28598000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr17:28572600-28590600	Weak transcription	Stomach Mucosa	stomach
11	chr17:28572600-28598000	Weak transcription	Small Intestine	intestine
12	chr17:28572800-28580200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:28573200-28577200	Strong transcription	Primary B cells from cord blood	blood
14	chr17:28573400-28581000	Strong transcription	Primary T cells from cord blood	blood
15	chr17:28573600-28576600	Strong transcription	HSMM	muscle
16	chr17:28573600-28576800	Strong transcription	K562	blood
17	chr17:28573600-28577000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr17:28573600-28577000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:28573600-28577000	Strong transcription	HUVEC	blood vessel
20	chr17:28573600-28577200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr17:28573600-28577400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:28573600-28580000	Strong transcription	Fetal Muscle Leg	muscle
23	chr17:28573600-28580600	Strong transcription	A549	lung
24	chr17:28573600-28588800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:28573600-28590800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:28573800-28576600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:28573800-28576800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr17:28573800-28595600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:28573800-28615400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr17:28574000-28576600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr17:28574000-28576800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr17:28574000-28576800	Strong transcription	Brain Anterior Caudate	brain
33	chr17:28574000-28576800	Strong transcription	GM12878-XiMat	blood
34	chr17:28574000-28577000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr17:28574000-28577000	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr17:28574000-28577000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr17:28574000-28580800	Strong transcription	Brain Hippocampus Middle	brain
38	chr17:28574000-28581600	Strong transcription	Dnd41	blood
39	chr17:28574000-28595200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr17:28574000-28616800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:28574200-28576400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr17:28574200-28577000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr17:28574200-28577000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr17:28574200-28577200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr17:28574200-28581000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr17:28574200-28581000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr17:28574200-28581800	Strong transcription	Fetal Thymus	thymus
48	chr17:28574400-28577400	Strong transcription	HepG2	liver
49	chr17:28574400-28579600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:28574400-28582200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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