Variant report

Variant	rs244415
Chromosome Location	chr16:69666683-69666684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69660423..69662352-chr16:69665460..69668239,3	MCF-7	breast:
2	chr16:69665807..69668565-chr16:69668796..69671600,3	K562	blood:
3	chr16:69665807..69668565-chr16:69668907..69671600,2	K562	blood:
4	chr16:69661329..69663803-chr16:69664795..69667678,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11640319	0.83[ASW][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap]
rs12446197	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12598642	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12599391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12923231	0.82[EUR][1000 genomes]
rs12924052	0.84[YRI][hapmap]
rs12929503	0.82[EUR][1000 genomes]
rs12933292	0.82[EUR][1000 genomes]
rs13330951	0.90[JPT][hapmap];0.83[MEX][hapmap]
rs1364063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1437134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1469908	0.82[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap]
rs2032912	0.83[EUR][1000 genomes]
rs2161630	0.83[ASW][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap]
rs244417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs244418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs244420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917670	0.87[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap]
rs2917677	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35967356	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3848278	0.83[ASW][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap]
rs4633710	0.82[YRI][hapmap]
rs4783721	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4783722	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62052816	0.82[EUR][1000 genomes]
rs6499240	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]
rs6499244	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669696	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187634	0.83[ASW][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs7191292	0.83[ASW][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs7192380	0.83[ASW][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap]
rs73568391	0.83[AFR][1000 genomes]
rs7359336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8049728	0.83[ASW][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap]
rs8055756	0.81[ASW][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap]
rs8061052	0.89[YRI][hapmap]
rs862320	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs889398	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs889399	0.96[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs244415	HSF4	cis	cerebellum	SCAN
rs244415	COG8	cis	cerebellum	SCAN
rs244415	DUS2L	cis	cerebellum	SCAN
rs244415	PDXDC2P	cis	parietal	SCAN
rs244415	LCAT	cis	parietal	SCAN
rs244415	AGRP	cis	cerebellum	SCAN
rs244415	TPPP3	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69624200-69669600	Weak transcription	Ovary	ovary
2	chr16:69645000-69669600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr16:69645400-69669800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr16:69645800-69669600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr16:69645800-69681000	Weak transcription	Fetal Brain Female	brain
6	chr16:69647200-69669000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr16:69647600-69670200	Weak transcription	Fetal Kidney	kidney
8	chr16:69647600-69705000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr16:69647800-69669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr16:69647800-69669200	Weak transcription	Adipose Nuclei	Adipose
11	chr16:69648000-69669200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr16:69648000-69669600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr16:69648400-69668400	Weak transcription	HMEC	breast
14	chr16:69648800-69668400	Weak transcription	Dnd41	blood
15	chr16:69650200-69670000	Weak transcription	Pancreas	Pancrea
16	chr16:69650200-69670200	Weak transcription	Gastric	stomach
17	chr16:69650200-69670200	Weak transcription	Spleen	Spleen
18	chr16:69650400-69669200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr16:69650600-69670000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:69653000-69668800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr16:69653600-69669400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr16:69653600-69669800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr16:69653600-69670000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr16:69653600-69680800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr16:69653600-69689600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr16:69653800-69669200	Weak transcription	Fetal Muscle Leg	muscle
27	chr16:69653800-69670000	Weak transcription	Right Ventricle	heart
28	chr16:69653800-69670000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr16:69653800-69670000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr16:69653800-69670200	Weak transcription	Brain Germinal Matrix	brain
31	chr16:69654000-69667400	Weak transcription	Colon Smooth Muscle	Colon
32	chr16:69654200-69669800	Weak transcription	Brain Anterior Caudate	brain
33	chr16:69654200-69670000	Weak transcription	Brain Hippocampus Middle	brain
34	chr16:69654200-69670200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr16:69654200-69703600	Weak transcription	Brain Angular Gyrus	brain
36	chr16:69654200-69705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr16:69654600-69705000	Weak transcription	Psoas Muscle	Psoas
38	chr16:69655000-69666800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr16:69655400-69667000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr16:69656000-69670600	Weak transcription	Small Intestine	intestine
41	chr16:69658800-69669000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr16:69659200-69670000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr16:69659800-69666800	Strong transcription	Placenta	Placenta
44	chr16:69659800-69669400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr16:69660000-69666800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr16:69660000-69669000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr16:69660200-69670200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr16:69660200-69670400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr16:69660200-69671800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr16:69660400-69670200	Weak transcription	NHLF	lung

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