Variant report

Variant	rs2215716
Chromosome Location	chr12:11044348-11044349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11042042..11044438-chr12:11050943..11053818,2	K562	blood:
2	chr12:11044254..11045058-chr12:11074291..11074831,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRH1-1	chr12:11044060-11044524	NONHSAT026908

Extended variants
information (count: 68 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1013312	0.86[EUR][1000 genomes]
rs10732561	0.85[EUR][1000 genomes]
rs10734843	0.83[EUR][1000 genomes]
rs10743929	0.86[EUR][1000 genomes]
rs10743930	0.86[EUR][1000 genomes]
rs10743936	0.82[EUR][1000 genomes]
rs10772371	0.86[EUR][1000 genomes]
rs10772392	0.87[EUR][1000 genomes]
rs10772395	0.88[EUR][1000 genomes]
rs10772398	0.88[EUR][1000 genomes]
rs10845224	0.86[EUR][1000 genomes]
rs11054053	0.86[EUR][1000 genomes]
rs11054054	0.86[EUR][1000 genomes]
rs12371547	0.86[EUR][1000 genomes]
rs12371728	1.00[ASN][1000 genomes]
rs1376249	0.85[EUR][1000 genomes]
rs1463237	0.85[EUR][1000 genomes]
rs1520225	0.86[EUR][1000 genomes]
rs1607694	0.86[EUR][1000 genomes]
rs16925194	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110097	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110098	0.84[EUR][1000 genomes]
rs2232956	1.00[ASN][1000 genomes]
rs2418105	1.00[ASN][1000 genomes]
rs2418214	0.86[EUR][1000 genomes]
rs2418215	0.86[EUR][1000 genomes]
rs2418218	0.90[EUR][1000 genomes]
rs2418223	0.87[EUR][1000 genomes]
rs2900550	1.00[ASN][1000 genomes]
rs2900552	0.86[EUR][1000 genomes]
rs2900577	0.85[EUR][1000 genomes]
rs34521533	1.00[ASN][1000 genomes]
rs3741843	0.87[EUR][1000 genomes]
rs3851578	1.00[ASN][1000 genomes]
rs3911150	1.00[CEU][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs4281556	0.86[EUR][1000 genomes]
rs4288845	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4388985	0.84[EUR][1000 genomes]
rs4763217	0.86[EUR][1000 genomes]
rs4763598	0.88[EUR][1000 genomes]
rs55748583	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55834906	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55862154	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621112	1.00[ASN][1000 genomes]
rs6488328	1.00[ASN][1000 genomes]
rs6488333	0.88[EUR][1000 genomes]
rs66679979	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666841	1.00[ASN][1000 genomes]
rs67458095	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684208	1.00[ASN][1000 genomes]
rs7297167	0.82[EUR][1000 genomes]
rs7299578	1.00[ASN][1000 genomes]
rs73045955	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73051630	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052447	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052449	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052454	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73053768	0.90[EUR][1000 genomes]
rs73053785	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054354	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054361	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054364	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306087	0.85[EUR][1000 genomes]
rs7315843	0.85[EUR][1000 genomes]
rs7486983	0.87[EUR][1000 genomes]
rs7978300	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2215716	LRRC23	cis	cerebellum	SCAN
rs2215716	TAS2R45	N/A	lymphoblastoid	RTeQTL
rs2215716	TAS2R8	cis	parietal	SCAN
rs2215716	PRH1	cis	multi-tissue	Pritchard
rs2215716	TAS2R43	cis	parietal	SCAN
rs2215716	TAS2R43	cis	cerebellum	SCAN
rs2215716	PRR4	cis	multi-tissue	Pritchard
rs2215716	TAS2R10	cis	parietal	SCAN
rs2215716	PRR4	cis	parietal	SCAN
rs2215716	TAS2R14	cis	cerebellum	SCAN
rs2215716	TAS2R48	Cis_1M	lymphoblastoid	RTeQTL
rs2215716	PRH1	cis	cerebellum	SCAN
rs2215716	TAS2R13	cis	cerebellum	SCAN
rs2215716	TAS2R9	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11009200-11045800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:11012200-11051800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:11012200-11055800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:11012200-11056200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:11014400-11052000	Weak transcription	Fetal Brain Male	brain
6	chr12:11020200-11045400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:11026000-11045800	Weak transcription	Brain Germinal Matrix	brain
8	chr12:11028400-11053400	Weak transcription	Brain Substantia Nigra	brain
9	chr12:11029200-11053200	Weak transcription	Fetal Brain Female	brain
10	chr12:11030600-11044400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:11030600-11044600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:11030600-11045800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:11030600-11046000	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:11030600-11051200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:11030600-11053400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:11030600-11053400	Weak transcription	Esophagus	oesophagus
17	chr12:11030600-11054200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:11031000-11049400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:11031000-11053200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:11031000-11055000	Weak transcription	Primary B cells from cord blood	blood
21	chr12:11031200-11044600	Weak transcription	Pancreas	Pancrea
22	chr12:11031600-11045400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:11032000-11053800	Weak transcription	Dnd41	blood
24	chr12:11033800-11101600	Weak transcription	Ovary	ovary
25	chr12:11034200-11046200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:11034600-11052000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:11034600-11059000	Weak transcription	Fetal Heart	heart
28	chr12:11034800-11044400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:11034800-11047400	Weak transcription	Adipose Nuclei	Adipose
30	chr12:11034800-11055200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:11036200-11045200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:11039200-11058000	Weak transcription	Aorta	Aorta
33	chr12:11039200-11070200	Weak transcription	Left Ventricle	heart
34	chr12:11039400-11044600	Weak transcription	Lung	lung
35	chr12:11039400-11048000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:11039400-11048200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:11043000-11046200	Enhancers	Fetal Intestine Large	intestine
38	chr12:11043400-11045000	Strong transcription	Primary T cells from cord blood	blood
39	chr12:11043400-11045800	Enhancers	Fetal Intestine Small	intestine
40	chr12:11043800-11047000	Enhancers	Liver	Liver
41	chr12:11043800-11055600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:11044000-11044400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:11044200-11044400	Enhancers	Gastric	stomach
44	chr12:11044200-11044600	Flanking Active TSS	HepG2	liver
45	chr12:11044200-11044800	Enhancers	Small Intestine	intestine
46	chr12:11044200-11045000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr12:11044200-11045800	Enhancers	Pancreatic Islets	Pancreatic Islet

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