Variant report

Variant	rs12465867
Chromosome Location	chr2:73612102-73612103
allele	C/T
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	FOXA2	chr2:73611974-73612296	HepG2	liver:	n/a	n/a
2	HCFC1	chr2:73612032-73614197	Hela-S3	cervix:	n/a	n/a
3	FOXA1	chr2:73611927-73612376	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:73460503..73462797-chr2:73611325..73612830,2	MCF-7	breast:
2	chr2:73460084..73462978-chr2:73611729..73614401,3	K562	blood:
3	chr2:73494646..73496647-chr2:73610262..73612844,2	MCF-7	breast:

Variant related genes	Relation type
ALMS1	TF binding region
ENSG00000135617	Chromatin interaction
ENSG00000135624	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10165862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10175529	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10190002	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs1083922	0.84[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs10865398	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs11126395	0.82[ASN][1000 genomes]
rs11126396	0.82[ASN][1000 genomes]
rs11126399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11693531	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898362	0.82[ASN][1000 genomes]
rs11899902	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13428235	0.83[AMR][1000 genomes]
rs1403412	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1406105	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs1522926	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1851546	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1852644	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1852647	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs1881246	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1881247	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2017116	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs2037814	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs2091022	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421489	0.90[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2421545	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2421546	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2901437	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35885918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820700	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs56672945	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60844734	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6546824	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546826	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546827	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6706235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6716776	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6728128	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6747145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749680	0.92[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs7560272	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7567017	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7567343	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7573275	0.83[ASN][1000 genomes]
rs7574291	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7576824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598901	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs7604588	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs780396	1.00[CHB][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2778	chr2:73596272-73615138	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12465867	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs12465867	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs12465867	PAIP2B	cis	cerebellum	SCAN
rs12465867	ALMS1P	cis	Whole Blood	GTEx
rs12465867	ALMS1	cis	cerebellum	SCAN
rs12465867	LRRTM4	cis	cerebellum	SCAN
rs12465867	ALMS1	cis	parietal	SCAN
rs12465867	ALMS1P	cis	cerebellum	SCAN
rs12465867	ALMS1P	cis	parietal	SCAN
rs12465867	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs12465867	ALMS1	cis	Whole Blood	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73611600-73612200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:73611600-73612200	Enhancers	Fetal Intestine Small	intestine
3	chr2:73612000-73612200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:73612000-73612200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:73612000-73612200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:73612000-73612200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr2:73612000-73612200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:73612000-73612200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:73612000-73612200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:73612000-73612200	Enhancers	Primary T cells from cord blood	blood
11	chr2:73612000-73612200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr2:73612000-73612200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:73612000-73612200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:73612000-73612200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr2:73612000-73612200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr2:73612000-73612200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:73612000-73612200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:73612000-73612200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr2:73612000-73612200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:73612000-73612200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:73612000-73612200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:73612000-73612200	Enhancers	Adipose Nuclei	Adipose
23	chr2:73612000-73612200	Enhancers	Liver	Liver
24	chr2:73612000-73612200	Enhancers	Brain Angular Gyrus	brain
25	chr2:73612000-73612200	Enhancers	Brain Anterior Caudate	brain
26	chr2:73612000-73612200	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr2:73612000-73612200	Enhancers	Brain Hippocampus Middle	brain
28	chr2:73612000-73612200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:73612000-73612200	Enhancers	Brain Substantia Nigra	brain
30	chr2:73612000-73612200	Enhancers	Duodenum Mucosa	Duodenum
31	chr2:73612000-73612200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr2:73612000-73612200	Enhancers	Fetal Heart	heart
33	chr2:73612000-73612200	Enhancers	Fetal Intestine Large	intestine
34	chr2:73612000-73612200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr2:73612000-73612200	Enhancers	Fetal Lung	lung
36	chr2:73612000-73612200	Enhancers	Fetal Muscle Leg	muscle
37	chr2:73612000-73612200	Enhancers	Rectal Smooth Muscle	rectum
38	chr2:73612000-73612200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr2:73612000-73612200	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr2:73612000-73612200	Flanking Active TSS	GM12878-XiMat	blood
41	chr2:73612000-73612200	Active TSS	HMEC	breast
42	chr2:73612000-73612200	Enhancers	Osteobl	bone
43	chr2:73612000-73612400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:73612000-73612400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:73612000-73612400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr2:73612000-73612400	Enhancers	Primary B cells from peripheral blood	blood
47	chr2:73612000-73612400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:73612000-73612400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:73612000-73612400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr2:73612000-73612400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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