Variant report

Variant	rs11126399
Chromosome Location	chr2:73613341-73613342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:73511465..73512045-chr2:73612502..73613373,2	K562	blood:
2	chr2:73497659..73500414-chr2:73612511..73614881,2	MCF-7	breast:
3	chr1:198125724..198126412-chr2:73612666..73613508,2	Hela-S3	cervix:
4	chr2:73613233..73615069-chr2:73661651..73663882,2	MCF-7	breast:
5	chr1:153508450..153509207-chr2:73613075..73613614,2	Hela-S3	cervix:
6	chr2:73596191..73598481-chr2:73612504..73614239,2	K562	blood:
7	chr2:73460084..73462978-chr2:73611729..73614401,3	K562	blood:
8	chr2:73612640..73613510-chr9:100684147..100685046,2	Hela-S3	cervix:
9	chr2:73612210..73615081-chr2:73714696..73716979,2	MCF-7	breast:
10	chr10:103911747..103912466-chr2:73612539..73613400,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000214484	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000135617	Chromatin interaction
ENSG00000151414	Chromatin interaction
ENSG00000221087	Chromatin interaction
ENSG00000166197	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000135624	Chromatin interaction
ENSG00000163013	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10165862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10175529	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10190002	1.00[CHB][hapmap]
rs1083922	0.84[CHB][hapmap]
rs10865398	1.00[CHB][hapmap]
rs11693531	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12465867	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]
rs1403412	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1406105	0.91[CHB][hapmap]
rs1522926	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1851546	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1852644	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1852647	1.00[CHB][hapmap]
rs1881246	1.00[CHB][hapmap]
rs1881247	1.00[CHB][hapmap]
rs2017116	1.00[CHB][hapmap]
rs2037814	1.00[CHB][hapmap]
rs2091022	0.83[EUR][1000 genomes]
rs2421489	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs2421545	1.00[CHB][hapmap]
rs2421546	1.00[CHB][hapmap]
rs2901437	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35885918	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3820700	1.00[CHB][hapmap]
rs6546824	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6546826	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs6546827	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6546829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap]
rs6706235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6710659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6716776	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6728128	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6747145	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]
rs6748040	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]
rs6749680	0.92[CHB][hapmap]
rs7560272	0.82[EUR][1000 genomes]
rs7567017	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7567343	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7574291	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs7576824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7598901	0.92[CHB][hapmap]
rs7604588	0.86[EUR][1000 genomes]
rs780390	1.00[CHB][hapmap]
rs780396	1.00[CHB][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11126399	ALMS1P	cis	Thyroid	GTEx
rs11126399	ALMS1	cis	Whole Blood	GTEx
rs11126399	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs11126399	ENSG00000116127	cis	multi-tissue	Pritchard
rs11126399	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73612000-73613400	Active TSS	Rectal Mucosa Donor 31	rectum
2	chr2:73612000-73614000	Active TSS	Colonic Mucosa	Colon
3	chr2:73612000-73614200	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr2:73612000-73614200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:73612000-73614200	Active TSS	NHDF-Ad	bronchial
6	chr2:73612000-73614600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr2:73612000-73615000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:73612000-73615200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr2:73612200-73613400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:73612200-73613800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:73612200-73613800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:73612200-73613800	Active TSS	Brain Cingulate Gyrus	brain
13	chr2:73612200-73613800	Active TSS	Colon Smooth Muscle	Colon
14	chr2:73612200-73613800	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr2:73612200-73613800	Active TSS	Fetal Thymus	thymus
16	chr2:73612200-73614000	Active TSS	Fetal Brain Male	brain
17	chr2:73612200-73614000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr2:73612200-73614000	Active TSS	Psoas Muscle	Psoas
19	chr2:73612200-73614200	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr2:73612200-73614200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:73612200-73614200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:73612200-73614200	Active TSS	Fetal Kidney	kidney
23	chr2:73612200-73614200	Active TSS	Fetal Muscle Trunk	muscle
24	chr2:73612200-73614200	Active TSS	HSMM	muscle
25	chr2:73612200-73614200	Active TSS	NHLF	lung
26	chr2:73612200-73614400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:73612200-73614400	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr2:73612200-73614400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:73612200-73614400	Active TSS	Right Ventricle	heart
30	chr2:73612200-73614400	Active TSS	HSMMtube	muscle
31	chr2:73612200-73614600	Active TSS	GM12878-XiMat	blood
32	chr2:73612200-73614800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:73612400-73613400	Active TSS	Primary B cells from cord blood	blood
34	chr2:73612400-73613400	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr2:73612400-73613600	Active TSS	Primary T cells from cord blood	blood
36	chr2:73612400-73613600	Active TSS	Placenta	Placenta
37	chr2:73612400-73613600	Active TSS	Stomach Smooth Muscle	stomach
38	chr2:73612400-73613800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:73612400-73613800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:73612400-73613800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:73612400-73613800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:73612400-73613800	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr2:73612400-73613800	Active TSS	Fetal Heart	heart
44	chr2:73612400-73613800	Active TSS	Stomach Mucosa	stomach
45	chr2:73612400-73613800	Active TSS	NH-A	brain
46	chr2:73612400-73613800	Active TSS	NHEK	skin
47	chr2:73612400-73614000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:73612400-73614000	Active TSS	Aorta	Aorta
49	chr2:73612400-73614000	Active TSS	Brain Substantia Nigra	brain
50	chr2:73612400-73614000	Active TSS	Esophagus	oesophagus

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