Variant report

Variant	rs1406105
Chromosome Location	chr2:73674261-73674262
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:73674241-73674476	IMR90	lung:	n/a	chr2:73674387-73674398 chr2:73674387-73674400 chr2:73674388-73674399 chr2:73674389-73674398
2	CEBPB	chr2:73674199-73674447	A549	lung:	n/a	chr2:73674387-73674398 chr2:73674387-73674400 chr2:73674388-73674399 chr2:73674389-73674398
3	CEBPB	chr2:73674256-73674452	K562	blood:	n/a	chr2:73674387-73674398 chr2:73674387-73674400 chr2:73674388-73674399 chr2:73674389-73674398

No.	Distal block	Cell Line	Cell type
1	chr2:73669090..73671630-chr2:73673489..73675228,2	K562	blood:
2	chr2:73673350..73675381-chr2:73675662..73678567,2	MCF-7	breast:
3	chr2:73663877..73666460-chr2:73672462..73674821,2	MCF-7	breast:
4	chr2:73672889..73674965-chr2:73680989..73682960,2	MCF-7	breast:

Variant related genes	Relation type
ALMS1	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10165862	0.91[CHB][hapmap]
rs10190002	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs10192125	0.97[ASN][1000 genomes]
rs10519309	0.91[ASN][1000 genomes]
rs1083922	0.91[CHD][hapmap]
rs10865398	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs1091568	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11126399	0.91[CHB][hapmap]
rs11685372	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1246096	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1246105	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12465867	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs12713783	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12995433	0.90[ASN][1000 genomes]
rs12996463	0.81[ASN][1000 genomes]
rs1403412	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs1852645	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1852646	0.88[ASN][1000 genomes]
rs1852647	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs1881246	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs1881247	0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1881248	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2017116	0.91[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2037814	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2091503	0.83[ASN][1000 genomes]
rs2091504	0.84[ASN][1000 genomes]
rs2178154	0.93[ASN][1000 genomes]
rs2280506	0.81[ASW][hapmap];0.95[GIH][hapmap]
rs2421489	0.83[CHB][hapmap]
rs2421545	0.91[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs2421546	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs2421548	0.90[ASN][1000 genomes]
rs2948441	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs3820700	0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MKK][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4852305	0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4852927	0.90[ASN][1000 genomes]
rs55677218	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56770679	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6546826	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs6546827	0.83[CHB][hapmap]
rs6546829	0.91[CHB][hapmap]
rs6546830	0.92[ASN][1000 genomes]
rs6546831	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546832	0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6546833	0.93[ASN][1000 genomes]
rs6546834	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6546842	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs66931335	0.96[AFR][1000 genomes]
rs6706235	0.91[CHB][hapmap]
rs6706409	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs6710659	0.91[CHB][hapmap]
rs6730785	0.86[ASN][1000 genomes]
rs6732440	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6734450	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6745560	0.93[CHD][hapmap]
rs6746458	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6746971	0.91[ASN][1000 genomes]
rs6747145	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs6748040	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs6749680	0.83[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs6759464	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs67877078	0.80[ASN][1000 genomes]
rs67898050	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68154245	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72811907	0.88[ASN][1000 genomes]
rs72811939	0.82[AFR][1000 genomes]
rs7574291	0.91[CHB][hapmap];0.87[CHD][hapmap]
rs7576824	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs7598901	0.83[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs7608308	0.80[ASN][1000 genomes]
rs780388	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs780389	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs780390	0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MKK][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs780391	0.82[ASN][1000 genomes]
rs780393	0.82[ASN][1000 genomes]
rs780396	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs802113	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1406105	DUSP11	cis	cerebellum	SCAN
rs1406105	ALMS1P	cis	cerebellum	SCAN
rs1406105	LOXL3	cis	cerebellum	SCAN
rs1406105	PDCD6IP	trans	cerebellum	SCAN
rs1406105	ALMS1P	cis	parietal	SCAN
rs1406105	DUSP11	cis	parietal	SCAN
rs1406105	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:122 , 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	chr2:73664600-73674600	Weak transcription	Brain Germinal Matrix	brain
32	chr2:73664600-73674600	Weak transcription	Esophagus	oesophagus
33	chr2:73664600-73675200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:73664600-73675200	Weak transcription	Brain Substantia Nigra	brain
35	chr2:73664600-73675200	Weak transcription	Lung	lung
36	chr2:73664600-73675400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:73664600-73675400	Weak transcription	Right Ventricle	heart
38	chr2:73664600-73676000	Weak transcription	GM12878-XiMat	blood
39	chr2:73664600-73683600	Weak transcription	A549	lung
40	chr2:73665000-73675200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:73665000-73675200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:73665000-73675200	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:73665000-73675200	Weak transcription	Small Intestine	intestine
44	chr2:73665000-73684400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:73665200-73674400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:73665200-73674600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:73665200-73674600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr2:73665200-73674600	Weak transcription	Thymus	Thymus
49	chr2:73665200-73675000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:73665200-73675200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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