Variant report

Variant	rs9753079
Chromosome Location	chr2:73733313-73733314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10170786	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183818	0.83[EUR][1000 genomes]
rs10184268	1.00[ASN][1000 genomes]
rs10186501	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.83[EUR][1000 genomes]
rs10187416	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189574	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	0.80[EUR][1000 genomes]
rs10193972	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195357	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195358	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197409	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199224	0.80[EUR][1000 genomes]
rs10207264	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209517	1.00[ASN][1000 genomes]
rs10496191	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496193	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	1.00[ASN][1000 genomes]
rs11126404	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11674602	0.84[EUR][1000 genomes]
rs11676385	0.84[EUR][1000 genomes]
rs11686019	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11689392	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693586	0.85[EUR][1000 genomes]
rs11693588	0.85[EUR][1000 genomes]
rs11884776	0.82[EUR][1000 genomes]
rs11901272	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903916	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384952	0.85[EUR][1000 genomes]
rs13385564	0.83[EUR][1000 genomes]
rs13391258	1.00[ASN][1000 genomes]
rs13392691	0.82[EUR][1000 genomes]
rs13392872	0.82[EUR][1000 genomes]
rs13398956	0.85[EUR][1000 genomes]
rs13400985	0.85[EUR][1000 genomes]
rs13409668	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411311	0.85[EUR][1000 genomes]
rs13421462	0.85[EUR][1000 genomes]
rs13427832	1.00[ASN][1000 genomes]
rs1403284	0.84[EUR][1000 genomes]
rs1534471	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881245	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918863	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056486	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140195	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421550	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421552	0.80[EUR][1000 genomes]
rs2421555	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	1.00[ASN][1000 genomes]
rs2901438	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500972	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56154726	0.85[EUR][1000 genomes]
rs58603761	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62151646	0.82[EUR][1000 genomes]
rs62151652	0.82[EUR][1000 genomes]
rs6546835	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546836	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546837	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546839	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546845	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546847	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546849	1.00[ASN][1000 genomes]
rs6546850	1.00[ASN][1000 genomes]
rs6546851	1.00[ASN][1000 genomes]
rs6546852	1.00[ASN][1000 genomes]
rs6546853	1.00[ASN][1000 genomes]
rs6546856	1.00[ASN][1000 genomes]
rs6546858	1.00[ASN][1000 genomes]
rs6546859	1.00[ASN][1000 genomes]
rs6546860	1.00[ASN][1000 genomes]
rs6546861	1.00[ASN][1000 genomes]
rs6704782	0.80[EUR][1000 genomes]
rs6705489	0.81[EUR][1000 genomes]
rs6705977	1.00[ASN][1000 genomes]
rs6707722	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708766	0.84[EUR][1000 genomes]
rs6711001	1.00[ASN][1000 genomes]
rs6711033	0.86[EUR][1000 genomes]
rs6718843	1.00[ASN][1000 genomes]
rs6719753	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723247	1.00[ASN][1000 genomes]
rs6724782	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726694	1.00[ASN][1000 genomes]
rs6736866	0.81[EUR][1000 genomes]
rs6740223	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745480	1.00[ASN][1000 genomes]
rs6753344	0.81[EUR][1000 genomes]
rs6756987	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73947808	0.85[EUR][1000 genomes]
rs7566364	1.00[ASN][1000 genomes]
rs7566385	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.85[EUR][1000 genomes]
rs7576245	1.00[ASN][1000 genomes]
rs7580750	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584575	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585004	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588169	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	0.81[EUR][1000 genomes]
rs7598396	0.81[EUR][1000 genomes]
rs7598946	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	0.83[EUR][1000 genomes]
rs7604682	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607014	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309473	0.82[EUR][1000 genomes]
rs9749859	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807961	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv874267	chr2:73717656-73857002	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9753079	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73707000-73733400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:73711800-73740400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:73713200-73757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:73715600-73740200	Weak transcription	Esophagus	oesophagus
5	chr2:73715600-73751800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:73715800-73740200	Weak transcription	Gastric	stomach
7	chr2:73717400-73757800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:73718000-73740800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:73718000-73746800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:73718200-73740400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:73718400-73738400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:73718400-73740200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:73718600-73740200	Weak transcription	Fetal Kidney	kidney
14	chr2:73718600-73740400	Weak transcription	Thymus	Thymus
15	chr2:73718800-73740200	Weak transcription	Aorta	Aorta
16	chr2:73718800-73740200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:73718800-73740400	Weak transcription	HSMMtube	muscle
18	chr2:73719000-73740200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:73719000-73740400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:73719200-73739800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:73719200-73740200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:73719400-73740400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:73719400-73747000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:73719600-73738200	Weak transcription	Primary T cells from cord blood	blood
25	chr2:73719800-73740200	Weak transcription	Primary B cells from cord blood	blood
26	chr2:73728200-73747000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:73731600-73740200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:73731600-73740200	Weak transcription	HSMM	muscle
29	chr2:73731600-73759000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:73731800-73739800	Weak transcription	Dnd41	blood
31	chr2:73731800-73740200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:73731800-73746800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:73731800-73752000	Weak transcription	Fetal Heart	heart
34	chr2:73731800-73807600	Weak transcription	Hela-S3	cervix
35	chr2:73732000-73740200	Weak transcription	Fetal Lung	lung
36	chr2:73732200-73735200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:73732200-73740800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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