Variant report

Variant	rs2178154
Chromosome Location	chr2:73661738-73661739
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	chr2:73613233..73615069-chr2:73661651..73663882,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10165862	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs10189578	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10190002	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10192125	0.96[ASN][1000 genomes]
rs10519309	0.91[ASN][1000 genomes]
rs1052161	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs1083919	0.93[EUR][1000 genomes]
rs1083921	0.92[EUR][1000 genomes]
rs1083922	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1083923	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865398	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1091568	0.81[ASN][1000 genomes]
rs11126399	0.92[CHB][hapmap]
rs11126402	0.88[EUR][1000 genomes]
rs11688718	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11890811	0.84[YRI][hapmap]
rs1246094	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1246096	0.82[ASN][1000 genomes]
rs1246105	0.84[ASN][1000 genomes]
rs12465867	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs12713783	0.96[ASN][1000 genomes]
rs12995433	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12996463	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13009035	0.83[EUR][1000 genomes]
rs1320374	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs13386124	0.89[EUR][1000 genomes]
rs13399087	0.88[EUR][1000 genomes]
rs1403412	0.92[CHB][hapmap]
rs1406105	0.83[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs1528169	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1852645	0.95[ASN][1000 genomes]
rs1852646	0.87[ASN][1000 genomes]
rs1852647	0.92[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1881246	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1881247	0.92[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1881248	0.91[ASN][1000 genomes]
rs2017116	0.92[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2037814	0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2091503	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2091504	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2140194	0.92[YRI][hapmap]
rs2421489	0.84[CHB][hapmap]
rs2421545	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421546	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2421548	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2421667	0.86[EUR][1000 genomes]
rs2948441	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs3820700	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs4346412	0.84[EUR][1000 genomes]
rs4852305	0.87[JPT][hapmap]
rs4852306	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4852308	0.83[EUR][1000 genomes]
rs4852927	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56770679	0.81[ASN][1000 genomes]
rs62153184	0.89[EUR][1000 genomes]
rs6546826	0.92[CHB][hapmap]
rs6546827	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs6546829	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs6546830	0.91[ASN][1000 genomes]
rs6546831	0.92[ASN][1000 genomes]
rs6546832	0.92[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6546833	0.92[ASN][1000 genomes]
rs6546834	0.96[ASN][1000 genomes]
rs6546842	0.81[ASN][1000 genomes]
rs6546846	0.85[EUR][1000 genomes]
rs6706235	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs6706409	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs6710659	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs6711285	0.85[YRI][hapmap]
rs6722867	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6729468	0.89[EUR][1000 genomes]
rs6730785	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6732440	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6734450	0.92[ASN][1000 genomes]
rs6743576	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6744697	0.91[EUR][1000 genomes]
rs6745560	0.96[CEU][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs6746458	0.96[ASN][1000 genomes]
rs6746971	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6747145	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs6748040	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs6749680	0.84[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6757996	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6759464	0.96[ASN][1000 genomes]
rs67898050	0.81[ASN][1000 genomes]
rs68154245	0.82[ASN][1000 genomes]
rs72811907	0.87[ASN][1000 genomes]
rs7562047	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7566315	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7571147	0.88[YRI][hapmap]
rs7574291	0.92[CHB][hapmap]
rs7576824	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs7585119	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7585663	0.85[YRI][hapmap]
rs7598660	0.87[CEU][hapmap]
rs7598901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7606483	0.90[EUR][1000 genomes]
rs7609249	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs780388	0.83[ASN][1000 genomes]
rs780389	0.83[ASN][1000 genomes]
rs780390	0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs780391	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs780393	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780394	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs780395	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs780396	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs802113	0.83[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2178154	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs2178154	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs2178154	ALMS1P	cis	Whole Blood	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73622800-73662800	Weak transcription	Right Ventricle	heart
2	chr2:73626800-73662600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:73626800-73662800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:73626800-73662800	Weak transcription	Aorta	Aorta
5	chr2:73626800-73663400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:73626800-73664000	Weak transcription	Thymus	Thymus
7	chr2:73627400-73664400	Weak transcription	Pancreas	Pancrea
8	chr2:73628800-73663000	Weak transcription	Hela-S3	cervix
9	chr2:73633200-73662800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:73634000-73663200	Weak transcription	Psoas Muscle	Psoas
11	chr2:73634400-73662000	Weak transcription	Lung	lung
12	chr2:73634400-73662800	Weak transcription	Esophagus	oesophagus
13	chr2:73634600-73661800	Weak transcription	Brain Germinal Matrix	brain
14	chr2:73637600-73662800	Weak transcription	Fetal Stomach	stomach
15	chr2:73637800-73662400	Weak transcription	A549	lung
16	chr2:73637800-73663600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:73637800-73676200	Weak transcription	Fetal Brain Male	brain
18	chr2:73639200-73675400	Weak transcription	HMEC	breast
19	chr2:73642200-73666000	Weak transcription	NHLF	lung
20	chr2:73643400-73663000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:73644600-73662800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:73645400-73662600	Weak transcription	Brain Substantia Nigra	brain
23	chr2:73645400-73675200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:73645600-73661800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:73645600-73663000	Weak transcription	NHDF-Ad	bronchial
26	chr2:73645600-73675200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:73645600-73676600	Weak transcription	NH-A	brain
28	chr2:73645600-73685600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:73645800-73662600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:73645800-73662800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:73646000-73664000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:73646200-73661800	Strong transcription	Dnd41	blood
33	chr2:73646200-73662800	Weak transcription	Brain Anterior Caudate	brain
34	chr2:73646400-73675200	Weak transcription	Osteobl	bone
35	chr2:73646600-73662600	Weak transcription	Fetal Brain Female	brain
36	chr2:73646600-73662800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:73646600-73663400	Weak transcription	Fetal Heart	heart
38	chr2:73646600-73664200	Weak transcription	Small Intestine	intestine
39	chr2:73646800-73662600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:73646800-73662800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:73646800-73663200	Weak transcription	HSMMtube	muscle
42	chr2:73647000-73684000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:73648400-73663200	Weak transcription	Fetal Kidney	kidney
44	chr2:73648600-73662600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:73649400-73663000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:73649600-73668000	Weak transcription	Gastric	stomach
47	chr2:73650200-73662800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:73651200-73662000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:73652000-73662800	Weak transcription	Fetal Thymus	thymus
50	chr2:73652000-73678400	Weak transcription	Muscle Satellite Cultured Cells	--

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