Variant report

Variant	rs10519309
Chromosome Location	chr2:73672629-73672630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73667000..73669186-chr2:73671276..73673472,2	K562	blood:
2	chr2:73672159..73673962-chr2:73674354..73675957,2	K562	blood:
3	chr2:73663877..73666460-chr2:73672462..73674821,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10165862	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs10190002	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs10192125	0.94[ASN][1000 genomes]
rs1052161	0.81[JPT][hapmap]
rs1083922	0.84[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs10865398	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs11126399	1.00[CHB][hapmap]
rs11684858	0.89[AMR][1000 genomes]
rs1246105	0.82[ASN][1000 genomes]
rs12465867	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap]
rs12713783	0.94[ASN][1000 genomes]
rs12995433	0.87[ASN][1000 genomes]
rs1320374	0.81[JPT][hapmap]
rs1403412	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1406105	0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1852645	0.93[ASN][1000 genomes]
rs1852646	0.85[ASN][1000 genomes]
rs1852647	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs1881246	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1881247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1881248	0.89[ASN][1000 genomes]
rs2017116	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2037814	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2091503	0.80[ASN][1000 genomes]
rs2091504	0.82[ASN][1000 genomes]
rs2178154	0.91[ASN][1000 genomes]
rs2421489	0.92[CHB][hapmap]
rs2421545	1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs2421546	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2421548	0.87[ASN][1000 genomes]
rs2948441	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3820700	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs4852305	0.86[JPT][hapmap]
rs4852927	0.87[ASN][1000 genomes]
rs6546826	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs6546827	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs6546829	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6546830	0.90[ASN][1000 genomes]
rs6546831	0.90[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs6546833	0.90[ASN][1000 genomes]
rs6546834	0.94[ASN][1000 genomes]
rs6706235	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6706409	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs6710659	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6730785	0.83[ASN][1000 genomes]
rs6732440	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6734450	0.90[ASN][1000 genomes]
rs6745560	0.84[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap]
rs6746458	0.94[ASN][1000 genomes]
rs6746971	0.88[ASN][1000 genomes]
rs6747145	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs6748040	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap]
rs6749680	0.92[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs6759464	0.94[ASN][1000 genomes]
rs68154245	0.80[ASN][1000 genomes]
rs72811907	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72811933	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7574291	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs7576824	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap]
rs7598901	0.92[CHB][hapmap];0.97[CHD][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs780388	0.81[ASN][1000 genomes]
rs780389	0.81[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap]
rs780396	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs802113	0.81[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10519309	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs10519309	ALMS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73637800-73676200	Weak transcription	Fetal Brain Male	brain
2	chr2:73639200-73675400	Weak transcription	HMEC	breast
3	chr2:73645400-73675200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:73645600-73675200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:73645600-73676600	Weak transcription	NH-A	brain
6	chr2:73645600-73685600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:73646400-73675200	Weak transcription	Osteobl	bone
8	chr2:73647000-73684000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:73652000-73678400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:73652200-73688400	Weak transcription	Colonic Mucosa	Colon
11	chr2:73657200-73675400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:73658400-73676600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:73659400-73675400	Weak transcription	Spleen	Spleen
14	chr2:73660200-73684400	Weak transcription	HUVEC	blood vessel
15	chr2:73663000-73674600	Weak transcription	Aorta	Aorta
16	chr2:73663000-73675200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:73663200-73675200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:73663200-73675200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:73663400-73675400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:73663400-73675400	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:73663600-73674600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:73663600-73680600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:73663800-73675200	Weak transcription	Psoas Muscle	Psoas
24	chr2:73663800-73689400	Weak transcription	NHDF-Ad	bronchial
25	chr2:73664000-73674600	Weak transcription	Hela-S3	cervix
26	chr2:73664200-73675200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:73664400-73674600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr2:73664400-73676000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:73664400-73678400	Weak transcription	K562	blood
30	chr2:73664400-73684200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:73664600-73673800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:73664600-73674600	Weak transcription	Brain Germinal Matrix	brain
33	chr2:73664600-73674600	Weak transcription	Esophagus	oesophagus
34	chr2:73664600-73675200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr2:73664600-73675200	Weak transcription	Brain Substantia Nigra	brain
36	chr2:73664600-73675200	Weak transcription	Lung	lung
37	chr2:73664600-73675400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:73664600-73675400	Weak transcription	Right Ventricle	heart
39	chr2:73664600-73676000	Weak transcription	GM12878-XiMat	blood
40	chr2:73664600-73683600	Weak transcription	A549	lung
41	chr2:73665000-73675200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:73665000-73675200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:73665000-73675200	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:73665000-73675200	Weak transcription	Small Intestine	intestine
45	chr2:73665000-73684400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:73665200-73674400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:73665200-73674600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:73665200-73674600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:73665200-73674600	Weak transcription	Thymus	Thymus
50	chr2:73665200-73675000	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links