Variant report

Variant	rs6499240
Chromosome Location	chr16:69686912-69686913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12446197	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12598642	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12599391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13330951	0.90[JPT][hapmap]
rs1364063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1437134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291959	0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs244415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs244418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs244420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917677	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2937121	0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs35967356	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4783721	1.00[CEU][hapmap]
rs4783722	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6499244	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669696	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8050414	0.85[CEU][hapmap]
rs862320	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs889398	0.96[CEU][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs889399	0.96[CEU][hapmap];0.90[JPT][hapmap]
rs9940315	0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6499240	TPPP3	cis	cerebellum	SCAN
rs6499240	LCAT	cis	parietal	SCAN
rs6499240	DUS2L	cis	cerebellum	SCAN
rs6499240	AGRP	cis	cerebellum	SCAN
rs6499240	PDXDC2P	cis	parietal	SCAN
rs6499240	COG8	cis	cerebellum	SCAN
rs6499240	HSF4	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69647600-69705000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr16:69653600-69689600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr16:69654200-69703600	Weak transcription	Brain Angular Gyrus	brain
4	chr16:69654200-69705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr16:69654600-69705000	Weak transcription	Psoas Muscle	Psoas
6	chr16:69660400-69709600	Weak transcription	Fetal Brain Male	brain
7	chr16:69667000-69727600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr16:69670600-69689200	Weak transcription	Brain Germinal Matrix	brain
9	chr16:69670800-69689600	Weak transcription	Esophagus	oesophagus
10	chr16:69670800-69715400	Weak transcription	Aorta	Aorta
11	chr16:69671200-69689600	Weak transcription	Spleen	Spleen
12	chr16:69671200-69726400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr16:69671400-69689400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr16:69678800-69705600	Weak transcription	Stomach Mucosa	stomach
15	chr16:69679400-69690400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr16:69680400-69699000	Strong transcription	Placenta	Placenta
17	chr16:69680400-69699200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr16:69680600-69691000	Strong transcription	HMEC	breast
19	chr16:69680600-69691000	Strong transcription	HUVEC	blood vessel
20	chr16:69680600-69699200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr16:69680800-69690800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr16:69680800-69691000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr16:69680800-69691000	Strong transcription	HepG2	liver
24	chr16:69680800-69691200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr16:69680800-69691200	Strong transcription	HSMM	muscle
26	chr16:69680800-69691400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr16:69680800-69691400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr16:69680800-69694400	Strong transcription	Fetal Lung	lung
29	chr16:69680800-69695800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr16:69680800-69698600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr16:69680800-69699000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr16:69680800-69699200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr16:69680800-69699200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr16:69680800-69699200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr16:69680800-69699200	Strong transcription	Liver	Liver
36	chr16:69681000-69691400	Strong transcription	Osteobl	bone
37	chr16:69681000-69697200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr16:69681000-69699200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr16:69681400-69687000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr16:69681400-69689400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr16:69681400-69689400	Weak transcription	Pancreas	Pancrea
42	chr16:69681400-69689600	Weak transcription	Colonic Mucosa	Colon
43	chr16:69681400-69689600	Weak transcription	Gastric	stomach
44	chr16:69681400-69689600	Weak transcription	Lung	lung
45	chr16:69681400-69705200	Weak transcription	Small Intestine	intestine
46	chr16:69681600-69687000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr16:69681600-69687000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr16:69681600-69687000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr16:69681600-69687000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr16:69681600-69687200	Weak transcription	Fetal Brain Female	brain

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