Variant report

Variant	rs2227296
Chromosome Location	chr12:11000934-11000935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1044682	0.88[EUR][1000 genomes]
rs1044683	0.88[EUR][1000 genomes]
rs10492100	0.86[EUR][1000 genomes]
rs10492101	0.86[EUR][1000 genomes]
rs10492102	0.86[EUR][1000 genomes]
rs10772380	0.91[EUR][1000 genomes]
rs10772383	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10772393	0.88[EUR][1000 genomes]
rs10772394	0.88[EUR][1000 genomes]
rs10845247	0.91[EUR][1000 genomes]
rs10845251	0.87[EUR][1000 genomes]
rs10845252	0.88[EUR][1000 genomes]
rs10845253	0.88[EUR][1000 genomes]
rs10845254	0.88[EUR][1000 genomes]
rs10845255	0.84[EUR][1000 genomes]
rs10845256	0.88[EUR][1000 genomes]
rs10845258	0.88[EUR][1000 genomes]
rs10845259	0.87[EUR][1000 genomes]
rs10845260	0.86[EUR][1000 genomes]
rs10845261	0.86[EUR][1000 genomes]
rs10845262	0.86[EUR][1000 genomes]
rs10845263	0.85[EUR][1000 genomes]
rs10845264	0.86[EUR][1000 genomes]
rs11054069	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11054082	0.87[EUR][1000 genomes]
rs11054084	0.88[EUR][1000 genomes]
rs11054088	0.87[EUR][1000 genomes]
rs11054089	0.88[EUR][1000 genomes]
rs11054090	0.88[EUR][1000 genomes]
rs11054092	0.88[EUR][1000 genomes]
rs11054093	0.88[EUR][1000 genomes]
rs11054094	0.88[EUR][1000 genomes]
rs11054095	0.88[EUR][1000 genomes]
rs11054096	0.84[EUR][1000 genomes]
rs11054097	0.88[EUR][1000 genomes]
rs11054098	0.88[EUR][1000 genomes]
rs11054099	0.88[EUR][1000 genomes]
rs11054101	0.88[EUR][1000 genomes]
rs11054102	0.88[EUR][1000 genomes]
rs11054103	0.87[EUR][1000 genomes]
rs11054104	0.88[EUR][1000 genomes]
rs11054105	0.88[EUR][1000 genomes]
rs11054106	0.88[EUR][1000 genomes]
rs11054107	0.88[EUR][1000 genomes]
rs11054108	0.88[EUR][1000 genomes]
rs11054109	0.88[EUR][1000 genomes]
rs11054110	0.87[EUR][1000 genomes]
rs11054111	0.87[EUR][1000 genomes]
rs11054112	0.87[EUR][1000 genomes]
rs11054113	0.87[EUR][1000 genomes]
rs11054114	0.86[EUR][1000 genomes]
rs11054115	0.86[EUR][1000 genomes]
rs11054116	0.86[EUR][1000 genomes]
rs11054117	0.87[EUR][1000 genomes]
rs11054118	0.87[EUR][1000 genomes]
rs11054119	0.87[EUR][1000 genomes]
rs11054121	0.87[EUR][1000 genomes]
rs11054122	0.87[EUR][1000 genomes]
rs11054123	0.86[EUR][1000 genomes]
rs11054124	0.86[EUR][1000 genomes]
rs11054125	0.86[EUR][1000 genomes]
rs11611410	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12367487	0.84[EUR][1000 genomes]
rs17742991	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17743605	0.88[EUR][1000 genomes]
rs17810798	0.88[EUR][1000 genomes]
rs2418224	0.88[EUR][1000 genomes]
rs3851583	0.86[EUR][1000 genomes]
rs3851586	0.85[EUR][1000 genomes]
rs3851589	0.87[EUR][1000 genomes]
rs4763599	0.88[EUR][1000 genomes]
rs61912245	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61912247	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61912249	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61914772	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61914773	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61914781	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61914783	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6488332	0.86[EUR][1000 genomes]
rs7134390	0.88[EUR][1000 genomes]
rs7134527	0.88[EUR][1000 genomes]
rs7137212	0.88[EUR][1000 genomes]
rs7137492	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7138108	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7138360	0.88[EUR][1000 genomes]
rs7138535	0.88[EUR][1000 genomes]
rs7298262	0.91[EUR][1000 genomes]
rs7302130	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302227	0.87[EUR][1000 genomes]
rs7303183	0.88[EUR][1000 genomes]
rs7305795	0.87[EUR][1000 genomes]
rs7308469	0.88[EUR][1000 genomes]
rs7308576	0.87[EUR][1000 genomes]
rs7312169	0.88[EUR][1000 genomes]
rs7398041	0.89[EUR][1000 genomes]
rs7966559	0.81[EUR][1000 genomes]
rs7979199	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049362	chr12:10893573-11018850	Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv898776	chr12:10909412-11032045	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs2227296	PRR4	cis	parietal	SCAN
rs2227296	PRR4	cis	lymphoblastoid	seeQTL
rs2227296	PRH2	cis	cerebellum	SCAN
rs2227296	PRH1	cis	cerebellum	SCAN
rs2227296	TAS2R19	cis	parietal	SCAN
rs2227296	TAS2R19	cis	cerebellum	SCAN
rs2227296	TAS2R50	cis	parietal	SCAN
rs2227296	PRR4	cis	lung	GTEx
rs2227296	TAS2R20	cis	parietal	SCAN
rs2227296	PRR4	cis	Heart Left Ventricle	GTEx
rs2227296	TAS2R31	cis	parietal	SCAN
rs2227296	TAS2R14	cis	parietal	SCAN
rs2227296	TAS2R13	cis	cerebellum	SCAN
rs2227296	TAS2R9	cis	cerebellum	SCAN
rs2227296	TAS2R14	cis	Esophagus Muscularis	GTEx
rs2227296	NANOGNB	cis	parietal	SCAN
rs2227296	TAS2R46	cis	cerebellum	SCAN
rs2227296	TAS2R14	cis	Nerve Tibial	GTEx
rs2227296	PRR4	cis	cerebellum	SCAN
rs2227296	PRR4	cis	Muscle Skeletal	GTEx
rs2227296	TAS2R43	cis	parietal	SCAN
rs2227296	TAS2R14	cis	cerebellum	SCAN
rs2227296	TAS2R50	cis	cerebellum	SCAN
rs2227296	TAS2R31	cis	cerebellum	SCAN
rs2227296	TAS2R10	cis	cerebellum	SCAN
rs2227296	TAS2R43	cis	cerebellum	SCAN
rs2227296	TAS2R13	cis	parietal	SCAN
rs2227296	TAS2R8	cis	cerebellum	SCAN
rs2227296	TAS2R20	cis	cerebellum	SCAN
rs2227296	RP11-434C1.1	cis	lung	GTEx
rs2227296	RP11-434C1.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10973600-11009600	Weak transcription	HSMM	muscle
2	chr12:10988400-11006000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10988400-11008400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:10988800-11001600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:10989200-11008600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:10989400-11008200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:10990000-11003800	Weak transcription	Right Ventricle	heart
8	chr12:10990000-11004000	Weak transcription	Fetal Heart	heart
9	chr12:10990000-11005400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:10990000-11005400	Weak transcription	Psoas Muscle	Psoas
11	chr12:10990000-11008400	Weak transcription	Fetal Lung	lung
12	chr12:10990200-11008400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:10991200-11007800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:10991200-11008000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:10991400-11010800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:10991600-11002000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr12:10993200-11008000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:10993600-11007600	Weak transcription	Fetal Intestine Small	intestine
19	chr12:10993800-11008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:10994000-11003800	Weak transcription	Primary B cells from cord blood	blood
21	chr12:10994000-11003800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:10994000-11007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:10994000-11008000	Weak transcription	Brain Germinal Matrix	brain
24	chr12:10994000-11008200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:10994000-11008400	Weak transcription	Brain Substantia Nigra	brain
26	chr12:10994000-11008400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:10994200-11002200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr12:10994200-11006000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:10994200-11008400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:10994200-11008400	Weak transcription	Thymus	Thymus
31	chr12:10994200-11008400	Weak transcription	HepG2	liver
32	chr12:10994200-11008600	Weak transcription	Spleen	Spleen
33	chr12:10994400-11001600	Weak transcription	Placenta	Placenta
34	chr12:10994400-11008400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:10994400-11035000	Weak transcription	Fetal Kidney	kidney
36	chr12:10994800-11008400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:10995600-11010800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:10995800-11005400	Weak transcription	GM12878-XiMat	blood
39	chr12:10995800-11005800	Weak transcription	Lung	lung
40	chr12:10995800-11008400	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:10996000-11003800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr12:10996800-11001800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:10997600-11008200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:10997800-11006200	Weak transcription	Small Intestine	intestine
45	chr12:10997800-11007400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:10998000-11004200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:10998000-11008200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr12:10998200-11007600	Weak transcription	Fetal Brain Female	brain
49	chr12:10998200-11008600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:10998600-11008400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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