Variant report

Variant	rs965243
Chromosome Location	chr12:11021008-11021009
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1013312	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047699	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10734841	0.94[ASN][1000 genomes]
rs10743927	0.94[ASN][1000 genomes]
rs10743929	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743930	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743931	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743936	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10772369	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772371	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772392	0.81[ASN][1000 genomes]
rs10845220	0.94[ASN][1000 genomes]
rs10845223	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845224	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845225	0.92[AFR][1000 genomes]
rs11054053	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054054	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12371547	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520225	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548804	0.94[ASN][1000 genomes]
rs1607694	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110097	0.84[CEU][hapmap]
rs2110098	0.82[AFR][1000 genomes];0.89[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]
rs2192139	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232958	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2298867	0.83[ASN][1000 genomes]
rs2418106	0.94[ASN][1000 genomes]
rs2418214	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418215	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418218	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2900552	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741843	0.81[ASN][1000 genomes]
rs3759250	0.91[ASN][1000 genomes]
rs3911150	0.84[CEU][hapmap]
rs4281556	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763217	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[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	0.89[EUR][1000 genomes]
rs654834	0.82[ASN][1000 genomes]
rs668521	0.82[ASN][1000 genomes]
rs7297167	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs741092	0.94[ASN][1000 genomes]
rs763839	0.94[ASN][1000 genomes]
rs7957888	0.94[ASN][1000 genomes]
rs7978300	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs953950	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs965243	PRR4	cis	Artery Tibial	GTEx
rs965243	LRRC23	cis	cerebellum	SCAN
rs965243	TAS2R9	cis	parietal	SCAN
rs965243	TAS2R43	cis	cerebellum	SCAN
rs965243	TAS2R14	cis	cerebellum	SCAN
rs965243	TAS2R45	N/A	lymphoblastoid	RTeQTL
rs965243	TAS2R13	cis	cerebellum	SCAN
rs965243	PRR4	cis	multi-tissue	Pritchard
rs965243	PRH1	cis	cerebellum	SCAN
rs965243	PRR4	cis	cerebellum	SCAN
rs965243	TAS2R43	cis	parietal	SCAN
rs965243	TAS2R15	cis	Thyroid	GTEx
rs965243	TAS2R20	cis	Skin Sun Exposed Lower leg	GTEx
rs965243	TAS2R48	Cis_1M	lymphoblastoid	RTeQTL
rs965243	TAS2R8	cis	parietal	SCAN
rs965243	TAS2R10	cis	parietal	SCAN
rs965243	PRH1	cis	multi-tissue	Pritchard
rs965243	GUCY2C	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

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	chr12:11007000-11038800	Weak transcription	Psoas Muscle	Psoas
5	chr12:11007200-11039400	Weak transcription	Right Ventricle	heart
6	chr12:11008800-11029400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:11008800-11030000	Weak transcription	HSMMtube	muscle
8	chr12:11009200-11029200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:11009200-11035200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:11009200-11045800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:11009600-11030000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:11011600-11030000	Weak transcription	Esophagus	oesophagus
13	chr12:11011800-11029800	Weak transcription	Liver	Liver
14	chr12:11011800-11030000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:11011800-11030000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:11011800-11031800	Weak transcription	Thymus	Thymus
17	chr12:11012000-11034200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:11012200-11031200	Weak transcription	Fetal Stomach	stomach
19	chr12:11012200-11051800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:11012200-11055800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:11012200-11056200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:11013200-11032800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr12:11014400-11025000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:11014400-11030000	Weak transcription	Ovary	ovary
25	chr12:11014400-11030000	Weak transcription	Pancreas	Pancrea
26	chr12:11014400-11043400	Weak transcription	Fetal Intestine Small	intestine
27	chr12:11014400-11052000	Weak transcription	Fetal Brain Male	brain
28	chr12:11015200-11029200	Weak transcription	Adipose Nuclei	Adipose
29	chr12:11015800-11029400	Weak transcription	Dnd41	blood
30	chr12:11016200-11030000	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:11016800-11030000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:11017000-11029400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:11019200-11029600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:11019200-11030200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:11019600-11021400	Strong transcription	Primary T cells from cord blood	blood
36	chr12:11019600-11029400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:11019600-11030000	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:11019800-11030000	Weak transcription	Primary B cells from cord blood	blood
39	chr12:11019800-11030000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:11019800-11030200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:11020200-11021400	Strong transcription	Primary hematopoietic stem cells	blood
42	chr12:11020200-11035800	Weak transcription	Brain Anterior Caudate	brain
43	chr12:11020200-11045400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:11020400-11021600	Strong transcription	Fetal Muscle Leg	muscle
45	chr12:11020800-11021200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:11020800-11021400	Strong transcription	Aorta	Aorta
47	chr12:11021000-11021400	Enhancers	Left Ventricle	heart
48	chr12:11021000-11021600	Enhancers	HepG2	liver

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