Variant report

Variant	rs2279072
Chromosome Location	chr19:44739399-44739400
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	chr19:44738727..44740500-chr19:44743424..44745617,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10405450	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10410086	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10423306	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10425945	0.96[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10775542	0.84[EUR][1000 genomes]
rs11667521	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs12460039	0.83[AFR][1000 genomes]
rs12462557	0.89[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs12462723	0.89[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs12975315	0.84[EUR][1000 genomes]
rs12975546	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs12980565	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2051059	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2085516	0.83[GIH][hapmap]
rs2125578	0.90[EUR][1000 genomes]
rs2125579	0.89[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs2168989	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2232801	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2279073	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2293587	0.83[GIH][hapmap];0.80[YRI][hapmap]
rs2356751	0.81[GIH][hapmap];0.81[YRI][hapmap]
rs3817595	0.83[GIH][hapmap];0.81[YRI][hapmap]
rs4802210	0.83[GIH][hapmap]
rs4802218	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs4803694	0.85[EUR][1000 genomes]
rs56357907	0.81[AFR][1000 genomes]
rs62117770	0.81[AFR][1000 genomes]
rs6509146	0.83[GIH][hapmap]
rs6509150	0.85[EUR][1000 genomes]
rs7248114	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7249209	0.81[GIH][hapmap]
rs7251682	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7253196	0.81[EUR][1000 genomes]
rs7253533	0.96[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7259916	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7260304	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8101032	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs8102037	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8105073	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs8106766	0.85[EUR][1000 genomes]
rs8109462	0.83[EUR][1000 genomes]
rs9304640	1.00[CEU][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9646642	0.86[EUR][1000 genomes]
rs9646643	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2279072	SIGLEC16	cis	cerebellum	SCAN
rs2279072	SAE1	cis	cerebellum	SCAN
rs2279072	SIX5	cis	cerebellum	SCAN
rs2279072	C5AR1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44717600-44739600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:44729800-44741000	ZNF genes & repeats	Lung	lung
3	chr19:44729800-44768600	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:44730000-44741200	ZNF genes & repeats	Ovary	ovary
5	chr19:44730000-44741400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
6	chr19:44730000-44742000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr19:44730000-44743600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:44730000-44745000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:44730000-44775600	ZNF genes & repeats	Liver	Liver
10	chr19:44730200-44739600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr19:44730200-44741200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:44730200-44741200	ZNF genes & repeats	Aorta	Aorta
13	chr19:44730200-44743000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
14	chr19:44730200-44743400	ZNF genes & repeats	Fetal Lung	lung
15	chr19:44730200-44754600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
16	chr19:44730400-44743400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:44730800-44739800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:44730800-44741000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:44731000-44739400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:44731000-44740800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:44731000-44742000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:44731000-44744400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
23	chr19:44731200-44739800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:44731200-44741400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
25	chr19:44731400-44739800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:44731400-44741400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
27	chr19:44731400-44742000	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr19:44731600-44739400	Strong transcription	HSMMtube	muscle
29	chr19:44731600-44739800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:44731600-44741000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
31	chr19:44731600-44741000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr19:44731600-44741200	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr19:44731600-44741200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
34	chr19:44731800-44739400	Strong transcription	Right Ventricle	heart
35	chr19:44731800-44741000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:44731800-44741000	ZNF genes & repeats	Small Intestine	intestine
37	chr19:44731800-44741200	Strong transcription	Placenta	Placenta
38	chr19:44731800-44741200	Strong transcription	Fetal Thymus	thymus
39	chr19:44731800-44741400	ZNF genes & repeats	Colon Smooth Muscle	Colon
40	chr19:44731800-44744200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr19:44732000-44739400	Strong transcription	Brain Cingulate Gyrus	brain
42	chr19:44732000-44739600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr19:44732000-44739600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:44732000-44741200	ZNF genes & repeats	Fetal Kidney	kidney
45	chr19:44732400-44739600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:44732400-44740400	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr19:44732400-44741400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:44732600-44741400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:44733000-44739800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr19:44733200-44739800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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