Variant report

Variant	rs35885918
Chromosome Location	chr2:73612234-73612235
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	E2F4	chr2:73612105-73613576	MCF10A-Er-Src	breast:	n/a	chr2:73612823-73612834
2	MAX	chr2:73612217-73614035	A549	lung:	n/a	n/a
3	FOXA2	chr2:73611974-73612296	HepG2	liver:	n/a	n/a
4	GTF3C2	chr2:73612187-73612797	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr2:73612130-73614979	SK-N-SH	brain:	n/a	n/a
6	HCFC1	chr2:73612032-73614197	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr2:73612160-73612267	MCF10A-Er-Src	breast:	n/a	n/a
8	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:
4	chr2:73612210..73615081-chr2:73714696..73716979,2	MCF-7	breast:

Variant related genes	Relation type
ALMS1	TF binding region
ENSG00000221087	Chromatin interaction
ENSG00000135624	Chromatin interaction
ENSG00000135617	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10165862	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]
rs11126395	0.82[ASN][1000 genomes]
rs11126396	0.82[ASN][1000 genomes]
rs11126399	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]
rs12465867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428235	0.83[AMR][1000 genomes]
rs1403412	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
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]
rs2091022	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2901437	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
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	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546827	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546829	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6706235	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706409	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710659	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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748040	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
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]
rs7576824	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604588	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]

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
rs35885918	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs35885918	ALMS1P	cis	Whole Blood	GTEx
rs35885918	ALMS1	cis	Whole Blood	GTEx
rs35885918	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs35885918	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73612000-73612400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:73612000-73612400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:73612000-73612400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:73612000-73612400	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:73612000-73612400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:73612000-73612400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:73612000-73612400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr2:73612000-73612400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:73612000-73612400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:73612000-73612400	Flanking Active TSS	K562	blood
11	chr2:73612000-73612600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:73612000-73612600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:73612000-73612600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr2:73612000-73612600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr2:73612000-73612600	Flanking Active TSS	Thymus	Thymus
16	chr2:73612000-73612600	Flanking Active TSS	A549	lung
17	chr2:73612000-73612600	Flanking Active TSS	Dnd41	blood
18	chr2:73612000-73612600	Flanking Active TSS	Hela-S3	cervix
19	chr2:73612000-73612600	Flanking Bivalent TSS/Enh	HepG2	liver
20	chr2:73612000-73612800	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr2:73612000-73612800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:73612000-73613400	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr2:73612000-73614000	Active TSS	Colonic Mucosa	Colon
24	chr2:73612000-73614200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr2:73612000-73614200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr2:73612000-73614200	Active TSS	NHDF-Ad	bronchial
27	chr2:73612000-73614600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr2:73612000-73615000	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr2:73612000-73615200	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr2:73612200-73612400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:73612200-73612400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:73612200-73612400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr2:73612200-73612400	Enhancers	Primary B cells from cord blood	blood
34	chr2:73612200-73612400	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr2:73612200-73612400	Active TSS	Primary T cells fromperipheralblood	blood
36	chr2:73612200-73612400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr2:73612200-73612400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr2:73612200-73612400	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr2:73612200-73612400	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr2:73612200-73612400	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr2:73612200-73612400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr2:73612200-73612400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:73612200-73612400	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr2:73612200-73612400	Flanking Active TSS	Fetal Heart	heart
45	chr2:73612200-73612400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr2:73612200-73612400	Enhancers	Stomach Mucosa	stomach
47	chr2:73612200-73612400	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr2:73612200-73612400	Flanking Active TSS	NH-A	brain
49	chr2:73612200-73612400	Flanking Active TSS	NHEK	skin
50	chr2:73612200-73612600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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