Variant report

Variant	rs11124576
Chromosome Location	chr2:37518716-37518717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10198835	0.86[CEU][hapmap]
rs11124578	0.93[CEU][hapmap]
rs11689186	0.87[CEU][hapmap];0.81[CHD][hapmap]
rs12622740	0.82[CHD][hapmap]
rs12712528	0.82[CHD][hapmap]
rs1477055	0.81[CEU][hapmap]
rs17409947	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481834	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2110963	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2160394	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2300881	0.81[CEU][hapmap]
rs2300884	0.81[CEU][hapmap]
rs2300885	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2300892	0.87[CEU][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2302650	0.87[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2302653	0.90[ASN][1000 genomes]
rs2888463	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770763	0.85[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3819892	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670192	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4670688	0.83[CEU][hapmap]
rs56059107	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59262093	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6726709	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72792835	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs876461	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9318	0.92[CEU][hapmap];0.81[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11124576	ATL2	cis	cerebellum	SCAN
rs11124576	CDC42EP3	cis	cerebellum	SCAN
rs11124576	EIF2AK2	cis	parietal	SCAN
rs11124576	QPCT	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37460200-37528600	Weak transcription	Stomach Mucosa	stomach
2	chr2:37461200-37518800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:37467600-37530200	Weak transcription	Pancreas	Pancrea
4	chr2:37470400-37521600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:37470800-37521400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:37479400-37520600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:37482800-37528600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:37484200-37539000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:37484600-37550400	Weak transcription	Right Ventricle	heart
10	chr2:37487200-37528600	Weak transcription	Brain Substantia Nigra	brain
11	chr2:37487600-37521200	Weak transcription	Brain Angular Gyrus	brain
12	chr2:37490600-37521000	Strong transcription	Dnd41	blood
13	chr2:37499200-37520800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:37499200-37521400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:37499200-37522200	Weak transcription	Spleen	Spleen
16	chr2:37499400-37522800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:37499400-37528600	Weak transcription	Brain Anterior Caudate	brain
18	chr2:37499400-37540200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr2:37500200-37529800	Weak transcription	Fetal Intestine Small	intestine
20	chr2:37500200-37530200	Weak transcription	Gastric	stomach
21	chr2:37500400-37519200	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:37500400-37520400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:37500600-37530200	Weak transcription	Thymus	Thymus
24	chr2:37502200-37528200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:37502200-37528600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:37502600-37520000	Weak transcription	Fetal Brain Female	brain
27	chr2:37502600-37521600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:37502600-37524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:37502600-37528600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:37502600-37532600	Weak transcription	Small Intestine	intestine
31	chr2:37502600-37533000	Weak transcription	Psoas Muscle	Psoas
32	chr2:37502600-37535800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:37502800-37528800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:37502800-37528800	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:37502800-37533800	Weak transcription	Lung	lung
36	chr2:37502800-37543400	Weak transcription	Esophagus	oesophagus
37	chr2:37505000-37521000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr2:37505600-37520400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:37509000-37550800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:37509600-37528600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:37509600-37539000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:37510200-37526600	Weak transcription	K562	blood
43	chr2:37510600-37536600	Weak transcription	Placenta	Placenta
44	chr2:37510800-37532200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:37511000-37533600	Weak transcription	Left Ventricle	heart
46	chr2:37511000-37550800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:37511200-37530200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:37511200-37534600	Weak transcription	HSMMtube	muscle
49	chr2:37511600-37520200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:37511800-37528600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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