Variant report

Variant	rs6749680
Chromosome Location	chr2:73685852-73685853
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCT7-2	chr2:73685068-73686609	ENSG00000230002.1
2	lnc-CCT7-2	chr2:73685068-73686611	ENSG00000230002.2
3	lnc-CCT7-2	chr2:73685068-73686604	NR_046762

Extended variants
information (count: 100 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10165862	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs10189578	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10190002	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10192125	0.85[ASN][1000 genomes]
rs1052161	0.84[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs1083919	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1083920	0.82[ASN][1000 genomes]
rs1083921	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1083922	0.81[ASW][hapmap];0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1083923	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865398	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11126399	0.92[CHB][hapmap]
rs11126402	0.84[EUR][1000 genomes]
rs11688718	0.83[EUR][1000 genomes]
rs1246094	0.83[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];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs12713783	0.85[ASN][1000 genomes]
rs12991161	0.84[CEU][hapmap]
rs12995433	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12996463	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13007607	0.81[AFR][1000 genomes]
rs13009035	0.95[AFR][1000 genomes]
rs13017182	0.81[AFR][1000 genomes]
rs13018422	0.81[AFR][1000 genomes]
rs13022145	0.81[AFR][1000 genomes]
rs1320374	0.83[ASW][hapmap];0.84[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.83[MKK][hapmap]
rs13386124	0.85[EUR][1000 genomes]
rs13399087	0.84[EUR][1000 genomes]
rs1403412	0.92[CHB][hapmap];0.94[CHD][hapmap]
rs1406105	0.83[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs1528169	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1852645	0.84[ASN][1000 genomes]
rs1852646	0.84[ASN][1000 genomes]
rs1852647	0.92[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1881246	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1881247	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1881248	0.84[ASN][1000 genomes]
rs2017116	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs2037814	0.92[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2091503	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2091504	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2178154	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2421489	0.83[CHB][hapmap]
rs2421545	0.84[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2421546	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2421548	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2421668	0.84[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap]
rs2948441	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs3820700	0.92[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs4852305	0.81[JPT][hapmap]
rs4852306	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4852308	1.00[AFR][1000 genomes]
rs4852927	0.89[ASN][1000 genomes]
rs4852930	0.81[AFR][1000 genomes]
rs4852951	0.84[CEU][hapmap]
rs4852954	0.85[MKK][hapmap]
rs4852957	0.81[AFR][1000 genomes]
rs4852959	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap]
rs62153184	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6546826	0.92[CHB][hapmap];0.97[CHD][hapmap]
rs6546827	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs6546829	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs6546830	0.88[ASN][1000 genomes]
rs6546831	0.85[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs6546833	0.82[ASN][1000 genomes]
rs6546834	0.85[ASN][1000 genomes]
rs6546846	0.81[EUR][1000 genomes]
rs6706235	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs6706409	0.92[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs6710659	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs6729468	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6730785	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6732440	0.81[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs6734450	0.85[ASN][1000 genomes]
rs6744697	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6745560	1.00[ASW][hapmap];0.81[CEU][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6746458	0.85[ASN][1000 genomes]
rs6746971	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6747145	0.92[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap]
rs6748040	0.92[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs6757996	0.82[EUR][1000 genomes]
rs6759464	0.85[ASN][1000 genomes]
rs68154245	0.81[ASN][1000 genomes]
rs7562047	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7566315	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7574291	0.92[CHB][hapmap];0.97[CHD][hapmap]
rs7576824	0.92[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs7585119	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7598660	0.83[MEX][hapmap]
rs7598901	1.00[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606483	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs780390	0.92[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs780391	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs780393	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780394	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs780395	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs780396	0.92[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6749680	ALMS1	cis	cerebellum	SCAN
rs6749680	MPHOSPH10	cis	cerebellum	SCAN
rs6749680	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs6749680	DUSP11	cis	cerebellum	SCAN
rs6749680	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6749680	MXD1	cis	cerebellum	SCAN
rs6749680	LRRTM4	cis	cerebellum	SCAN
rs6749680	ALMS1P	cis	cerebellum	SCAN
rs6749680	ALMS1	cis	parietal	SCAN
rs6749680	ALMS1P	cis	parietal	SCAN
rs6749680	DUSP11	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73652200-73688400	Weak transcription	Colonic Mucosa	Colon
2	chr2:73663800-73689400	Weak transcription	NHDF-Ad	bronchial
3	chr2:73673000-73687200	Weak transcription	NHEK	skin
4	chr2:73675800-73688800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:73676200-73719400	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:73676600-73687200	Weak transcription	Esophagus	oesophagus
7	chr2:73676800-73687600	Weak transcription	Brain Substantia Nigra	brain
8	chr2:73676800-73688000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:73676800-73706400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:73677000-73688000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:73677000-73688400	Weak transcription	Psoas Muscle	Psoas
12	chr2:73677000-73698000	Weak transcription	Hela-S3	cervix
13	chr2:73677000-73714200	Weak transcription	Pancreas	Pancrea
14	chr2:73677200-73687200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:73677200-73689000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:73677200-73689200	Weak transcription	Osteobl	bone
17	chr2:73677400-73686800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:73677400-73687600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:73677800-73686800	Weak transcription	Small Intestine	intestine
20	chr2:73677800-73688200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:73678000-73688400	Weak transcription	Spleen	Spleen
22	chr2:73678000-73706800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:73678200-73687200	Weak transcription	Right Ventricle	heart
24	chr2:73678400-73686800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:73678600-73686600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:73678600-73686800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:73678600-73686800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:73678600-73687600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:73678600-73688400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:73678800-73687000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:73678800-73687400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:73678800-73688400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:73679200-73697000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:73679600-73686600	Weak transcription	Thymus	Thymus
35	chr2:73679600-73687400	Weak transcription	Lung	lung
36	chr2:73679600-73688000	Weak transcription	HSMMtube	muscle
37	chr2:73679800-73692600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:73680000-73689600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:73680200-73706400	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:73680200-73714200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:73680400-73688600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:73680400-73689200	Weak transcription	NH-A	brain
43	chr2:73680600-73687000	Weak transcription	Placenta	Placenta
44	chr2:73680600-73687600	Weak transcription	Fetal Stomach	stomach
45	chr2:73680800-73686000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:73680800-73687400	Weak transcription	Primary B cells from cord blood	blood
47	chr2:73681000-73688600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:73681200-73686800	Weak transcription	Fetal Thymus	thymus
49	chr2:73681200-73687400	Weak transcription	HepG2	liver
50	chr2:73681600-73706800	Weak transcription	HSMM	muscle

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