Variant report

Variant	rs12447326
Chromosome Location	chr16:69630853-69630854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69630299..69632744-chr16:69635847..69638024,2	K562	blood:
2	chr16:69624364..69627243-chr16:69629072..69631620,3	K562	blood:
3	chr16:69626084..69628621-chr16:69630498..69632392,2	MCF-7	breast:
4	chr16:69599613..69601834-chr16:69628546..69631333,2	MCF-7	breast:
5	chr16:69622847..69627243-chr16:69629072..69632922,5	K562	blood:

Variant related genes	Relation type
ENSG00000102908	Chromatin interaction
ENSG00000223109	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10048108	0.83[ASN][1000 genomes]
rs10163235	0.83[ASN][1000 genomes]
rs10454066	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10500551	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs10852457	0.94[ASN][1000 genomes]
rs10852458	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11075727	0.88[ASN][1000 genomes]
rs11075728	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11075730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11639947	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs11641050	0.96[ASN][1000 genomes]
rs11641233	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs11642030	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11642115	0.96[ASN][1000 genomes]
rs11643240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643530	0.99[ASN][1000 genomes]
rs11646884	0.90[ASN][1000 genomes]
rs11648249	0.88[ASN][1000 genomes]
rs12232410	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12447883	0.80[ASN][1000 genomes]
rs12449005	0.99[ASN][1000 genomes]
rs12595869	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs12595878	0.99[ASN][1000 genomes]
rs12596823	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13337236	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1437135	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1437136	0.90[ASN][1000 genomes]
rs16958970	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs16959035	0.86[ASN][1000 genomes]
rs1800566	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs1865965	0.83[ASN][1000 genomes]
rs2118220	0.90[ASN][1000 genomes]
rs2161631	0.81[JPT][hapmap]
rs2196574	0.84[ASN][1000 genomes]
rs2217950	0.90[ASN][1000 genomes]
rs2361838	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs3169315	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs3743673	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3885612	0.99[ASN][1000 genomes]
rs55751101	0.99[ASN][1000 genomes]
rs56316408	0.91[ASN][1000 genomes]
rs57488237	0.83[ASN][1000 genomes]
rs57565297	0.83[ASN][1000 genomes]
rs60010276	0.88[ASN][1000 genomes]
rs60099379	0.83[ASN][1000 genomes]
rs60472033	0.90[ASN][1000 genomes]
rs61310815	0.88[ASN][1000 genomes]
rs61460899	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6499239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6499255	0.82[MEX][hapmap]
rs689455	0.84[ASN][1000 genomes]
rs7186002	0.84[ASN][1000 genomes]
rs7190652	0.96[ASN][1000 genomes]
rs7194753	0.82[CHD][hapmap];0.82[MEX][hapmap]
rs7196943	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7198242	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs7200935	0.84[CHD][hapmap];0.82[MEX][hapmap]
rs72783115	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74026882	0.99[ASN][1000 genomes]
rs8045142	0.90[ASN][1000 genomes]
rs8045705	0.84[ASN][1000 genomes]
rs8046314	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8047885	0.88[ASN][1000 genomes]
rs8052086	0.90[ASN][1000 genomes]
rs8053080	0.90[ASN][1000 genomes]
rs8054000	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8054096	0.88[ASN][1000 genomes]
rs8060588	0.91[ASN][1000 genomes]
rs920191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788803	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788837	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs9921045	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs9929720	0.84[CHD][hapmap];0.82[MEX][hapmap]
rs9933526	0.83[ASN][1000 genomes]
rs9940548	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12447326	TPPP3	cis	parietal	SCAN
rs12447326	CES2	cis	cerebellum	SCAN
rs12447326	SLC7A6	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69602000-69633000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr16:69602200-69631600	Weak transcription	Pancreas	Pancrea
3	chr16:69602200-69643200	Weak transcription	Fetal Muscle Leg	muscle
4	chr16:69602200-69646600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr16:69602200-69653600	Weak transcription	Fetal Thymus	thymus
6	chr16:69603000-69647400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr16:69603600-69660000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr16:69605400-69663200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr16:69605600-69660600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr16:69610800-69642000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr16:69611200-69645600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr16:69612400-69643800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr16:69614000-69643200	Weak transcription	Colon Smooth Muscle	Colon
14	chr16:69614000-69644400	Weak transcription	Adipose Nuclei	Adipose
15	chr16:69617600-69653400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr16:69617800-69646600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr16:69619800-69644800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr16:69621400-69640200	Weak transcription	Fetal Stomach	stomach
19	chr16:69622200-69645400	Weak transcription	Spleen	Spleen
20	chr16:69622400-69642000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr16:69622600-69644400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr16:69623800-69646800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr16:69624000-69633600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr16:69624000-69646800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr16:69624200-69638200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr16:69624200-69669600	Weak transcription	Ovary	ovary
27	chr16:69624800-69631200	Weak transcription	GM12878-XiMat	blood
28	chr16:69624800-69642200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr16:69626200-69632000	Weak transcription	Dnd41	blood
30	chr16:69627000-69645400	Weak transcription	Placenta	Placenta
31	chr16:69627600-69642800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr16:69627600-69648000	Weak transcription	Lung	lung
33	chr16:69628000-69634200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr16:69628200-69632600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr16:69628200-69633600	Weak transcription	Brain Substantia Nigra	brain
36	chr16:69628400-69643200	Weak transcription	HSMM	muscle
37	chr16:69629000-69631400	Enhancers	Fetal Intestine Small	intestine
38	chr16:69629000-69632000	Weak transcription	Left Ventricle	heart
39	chr16:69629000-69637200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr16:69629000-69641000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr16:69629200-69660000	Weak transcription	Primary B cells from cord blood	blood
42	chr16:69629400-69631800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr16:69629400-69632000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr16:69629400-69632000	Weak transcription	Right Ventricle	heart
45	chr16:69629400-69632600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr16:69629400-69646600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr16:69629400-69648000	Weak transcription	Esophagus	oesophagus
48	chr16:69629400-69648000	Weak transcription	Right Atrium	heart
49	chr16:69629600-69631200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr16:69629600-69632600	Weak transcription	Brain Hippocampus Middle	brain

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