Variant report

Variant	rs12066445
Chromosome Location	chr1:151740420-151740421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr1:151740364-151741230	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151739515..151742335-chr1:151761325..151763693,2	MCF-7	breast:
2	chr1:151680360..151683089-chr1:151739535..151742461,2	MCF-7	breast:
3	chr1:151738680..151741094-chr1:151741696..151744217,2	K562	blood:
4	chr1:151740105..151741815-chr1:151762387..151764682,2	MCF-7	breast:

Variant related genes	Relation type
MRPL9	TF binding region
OAZ3	TF binding region
ENSG00000268288	TF binding region
ENSG00000182134	Chromatin interaction
ENSG00000159409	Chromatin interaction
ENSG00000203288	Chromatin interaction
ENSG00000249602	Chromatin interaction
ENSG00000240510	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10888435	0.88[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs11204885	0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11204887	0.92[EUR][1000 genomes]
rs11204888	0.92[EUR][1000 genomes]
rs12073999	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12409493	0.93[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes]
rs12567867	0.89[EUR][1000 genomes]
rs1781419	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2293088	0.88[CEU][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs33911740	0.91[EUR][1000 genomes]
rs3748612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3923394	0.96[CEU][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs4845572	0.92[EUR][1000 genomes]
rs6667279	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679233	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs7534811	0.88[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs868868	0.81[ASW][hapmap];0.88[CEU][hapmap];0.84[CHB][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs9017	0.84[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs9826	0.88[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12066445	LINGO4	cis	cerebellum	SCAN
rs12066445	TDRKH	cis	cerebellum	SCAN
rs12066445	TDRKH	Cis_1M	lymphoblastoid	RTeQTL
rs12066445	BCL9	cis	cerebellum	SCAN
rs12066445	S100A13	cis	cerebellum	SCAN
rs12066445	TDRKH	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151736600-151741800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:151736600-151746200	Weak transcription	Thymus	Thymus
3	chr1:151736600-151746600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:151736600-151751000	Weak transcription	Ovary	ovary
5	chr1:151736800-151745400	Weak transcription	Fetal Brain Female	brain
6	chr1:151736800-151745800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:151736800-151745800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:151736800-151745800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:151736800-151746000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:151736800-151746000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:151736800-151746200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:151736800-151746200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:151736800-151746200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:151736800-151746200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:151736800-151746200	Weak transcription	Brain Anterior Caudate	brain
16	chr1:151736800-151746200	Weak transcription	Fetal Thymus	thymus
17	chr1:151736800-151746400	Weak transcription	Aorta	Aorta
18	chr1:151736800-151746400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:151736800-151746400	Weak transcription	Right Ventricle	heart
20	chr1:151736800-151746600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:151736800-151746600	Weak transcription	Psoas Muscle	Psoas
22	chr1:151736800-151746800	Weak transcription	Left Ventricle	heart
23	chr1:151736800-151746800	Weak transcription	Spleen	Spleen
24	chr1:151736800-151747200	Weak transcription	Fetal Brain Male	brain
25	chr1:151736800-151747400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:151736800-151747800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:151736800-151748000	Weak transcription	Colonic Mucosa	Colon
28	chr1:151736800-151750800	Weak transcription	Right Atrium	heart
29	chr1:151736800-151762600	Weak transcription	Gastric	stomach
30	chr1:151737000-151740600	Weak transcription	Adipose Nuclei	Adipose
31	chr1:151737000-151740600	Weak transcription	Fetal Heart	heart
32	chr1:151737000-151740600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:151737000-151742400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:151737000-151742600	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:151737000-151743000	Weak transcription	Primary T cells from cord blood	blood
36	chr1:151737000-151745200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:151737000-151745400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:151737000-151745600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:151737000-151745800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:151737000-151745800	Weak transcription	Liver	Liver
41	chr1:151737000-151745800	Weak transcription	Brain Germinal Matrix	brain
42	chr1:151737000-151745800	Weak transcription	Brain Substantia Nigra	brain
43	chr1:151737000-151746000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:151737000-151746000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:151737000-151746200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:151737000-151746200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:151737000-151746400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:151737000-151746400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:151737000-151746400	Weak transcription	Brain Angular Gyrus	brain
50	chr1:151737000-151746400	Weak transcription	Brain Cingulate Gyrus	brain

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