Variant report

Variant	rs2192139
Chromosome Location	chr12:11012676-11012677
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1013312	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047699	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10734841	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10743927	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10743929	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743930	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743931	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743936	0.86[ASN][1000 genomes]
rs10772369	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772371	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772392	0.81[ASN][1000 genomes]
rs10845220	0.94[ASN][1000 genomes]
rs10845223	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845224	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845225	0.92[AFR][1000 genomes]
rs11054053	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054054	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12371547	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520225	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548804	0.94[ASN][1000 genomes]
rs1607694	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110098	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159899	0.94[ASN][1000 genomes]
rs2159900	0.97[ASN][1000 genomes]
rs2232958	0.91[ASN][1000 genomes]
rs2298867	0.83[ASN][1000 genomes]
rs2418106	0.94[ASN][1000 genomes]
rs2418214	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418215	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418218	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2900552	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741843	0.81[ASN][1000 genomes]
rs3759250	0.91[ASN][1000 genomes]
rs4281556	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763217	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58051461	0.91[ASN][1000 genomes]
rs58836988	0.86[ASN][1000 genomes]
rs592864	0.82[ASN][1000 genomes]
rs60547308	0.91[ASN][1000 genomes]
rs60652912	0.82[ASN][1000 genomes]
rs612456	0.82[ASN][1000 genomes]
rs640372	0.82[ASN][1000 genomes]
rs646494	0.82[ASN][1000 genomes]
rs6488331	0.87[EUR][1000 genomes]
rs654834	0.82[ASN][1000 genomes]
rs668521	0.82[ASN][1000 genomes]
rs7297167	0.89[ASN][1000 genomes]
rs741092	0.94[ASN][1000 genomes]
rs763839	0.94[ASN][1000 genomes]
rs7957888	0.94[ASN][1000 genomes]
rs7978300	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs953950	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs965243	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2192139	PRR4	cis	Thyroid	GTEx
rs2192139	TAS2R48	Cis_1M	lymphoblastoid	RTeQTL
rs2192139	TAS2R20	cis	Skin Sun Exposed Lower leg	GTEx
rs2192139	TAS2R45	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10994400-11035000	Weak transcription	Fetal Kidney	kidney
2	chr12:10998600-11034800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:10999000-11029200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:11004400-11014200	Weak transcription	Gastric	stomach
5	chr12:11006600-11014200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:11007000-11038800	Weak transcription	Psoas Muscle	Psoas
7	chr12:11007200-11039400	Weak transcription	Right Ventricle	heart
8	chr12:11008800-11014000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:11008800-11014000	Weak transcription	Brain Substantia Nigra	brain
10	chr12:11008800-11029400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:11008800-11030000	Weak transcription	HSMMtube	muscle
12	chr12:11009000-11012800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:11009000-11012800	Weak transcription	Hela-S3	cervix
14	chr12:11009200-11013200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:11009200-11013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:11009200-11029200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:11009200-11035200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:11009200-11045800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:11009600-11030000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:11009800-11014200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:11010600-11012800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr12:11011400-11013800	Weak transcription	Spleen	Spleen
23	chr12:11011400-11014000	Weak transcription	Pancreas	Pancrea
24	chr12:11011400-11014200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:11011600-11013600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:11011600-11014000	Weak transcription	Fetal Brain Male	brain
27	chr12:11011600-11014000	Weak transcription	Fetal Lung	lung
28	chr12:11011600-11030000	Weak transcription	Esophagus	oesophagus
29	chr12:11011800-11013600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:11011800-11014000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:11011800-11029800	Weak transcription	Liver	Liver
32	chr12:11011800-11030000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:11011800-11030000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:11011800-11031800	Weak transcription	Thymus	Thymus
35	chr12:11012000-11013600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:11012000-11013800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr12:11012000-11013800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:11012000-11014000	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:11012000-11014200	Weak transcription	Left Ventricle	heart
40	chr12:11012000-11014800	Weak transcription	Brain Angular Gyrus	brain
41	chr12:11012000-11021000	Weak transcription	HepG2	liver
42	chr12:11012000-11034200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:11012200-11013000	Weak transcription	Primary T cells from cord blood	blood
44	chr12:11012200-11013400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:11012200-11013800	Weak transcription	Adipose Nuclei	Adipose
46	chr12:11012200-11013800	Weak transcription	Brain Anterior Caudate	brain
47	chr12:11012200-11013800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:11012200-11014000	Weak transcription	Aorta	Aorta
49	chr12:11012200-11014000	Weak transcription	Fetal Intestine Small	intestine
50	chr12:11012200-11014000	Weak transcription	Fetal Muscle Leg	muscle

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