Variant report

Variant	rs2300885
Chromosome Location	chr2:37496276-37496277
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37488659..37490185-chr2:37494885..37496985,2	K562	blood:
2	chr2:37486999..37491157-chr2:37494189..37497497,3	MCF-7	breast:
3	chr2:37493948..37499584-chr2:37500018..37504344,8	K562	blood:

Variant related genes	Relation type
ENSG00000115825	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10198835	1.00[CEU][hapmap]
rs11124576	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]
rs11689186	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs12622740	0.89[CHB][hapmap];0.89[CHD][hapmap]
rs12712528	0.94[CHB][hapmap];0.89[CHD][hapmap]
rs1477055	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs17409947	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17481834	1.00[ASW][hapmap];0.93[CEU][hapmap];0.81[CHD][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2110963	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2160394	1.00[CEU][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2268987	0.83[TSI][hapmap]
rs2300881	0.81[CEU][hapmap]
rs2300884	0.81[CEU][hapmap]
rs2300892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2302650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770763	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3819892	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4670192	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55991517	0.94[EUR][1000 genomes]
rs56059107	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61208496	0.94[EUR][1000 genomes]
rs6726709	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6743961	0.94[CHB][hapmap]
rs72792821	0.94[EUR][1000 genomes]
rs72792835	0.91[EUR][1000 genomes]
rs876461	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9318	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2300885	QPCT	cis	parietal	SCAN
rs2300885	ATL2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37460000-37501600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:37460200-37528600	Weak transcription	Stomach Mucosa	stomach
3	chr2:37460400-37498600	Weak transcription	Gastric	stomach
4	chr2:37460600-37498600	Weak transcription	Spleen	Spleen
5	chr2:37461200-37518800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:37463400-37509600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:37467600-37530200	Weak transcription	Pancreas	Pancrea
8	chr2:37470400-37498600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:37470400-37521600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:37470800-37521400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:37476800-37501400	Weak transcription	Esophagus	oesophagus
12	chr2:37477400-37502200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:37479400-37520600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:37479800-37501600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:37480600-37505000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:37481600-37500800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:37482600-37497800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:37482600-37501800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:37482800-37498600	Weak transcription	Lung	lung
20	chr2:37482800-37528600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:37483400-37498600	Weak transcription	HSMMtube	muscle
22	chr2:37483600-37498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:37484200-37501600	Weak transcription	K562	blood
24	chr2:37484200-37539000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:37484400-37511600	Weak transcription	Fetal Brain Male	brain
26	chr2:37484600-37498600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:37484600-37498600	Weak transcription	NHEK	skin
28	chr2:37484600-37500000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:37484600-37500400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:37484600-37501400	Weak transcription	Colonic Mucosa	Colon
31	chr2:37484600-37550400	Weak transcription	Right Ventricle	heart
32	chr2:37484800-37498600	Weak transcription	Aorta	Aorta
33	chr2:37486200-37501600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:37486400-37501200	Weak transcription	Psoas Muscle	Psoas
35	chr2:37486600-37497800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:37486600-37499000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:37486800-37496800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:37486800-37498400	Weak transcription	Ovary	ovary
39	chr2:37487200-37528600	Weak transcription	Brain Substantia Nigra	brain
40	chr2:37487600-37521200	Weak transcription	Brain Angular Gyrus	brain
41	chr2:37489200-37500000	Strong transcription	NHDF-Ad	bronchial
42	chr2:37490400-37498400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:37490400-37498600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:37490400-37503400	Strong transcription	Liver	Liver
45	chr2:37490400-37507000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:37490400-37510800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:37490600-37521000	Strong transcription	Dnd41	blood
48	chr2:37491000-37503200	Strong transcription	Fetal Muscle Leg	muscle
49	chr2:37491000-37512400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:37491200-37497200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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