Variant report

Variant	rs7596773
Chromosome Location	chr2:73846000-73846001
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73839411..73842027-chr2:73845184..73847412,3	MCF-7	breast:
2	chr2:73842404..73844324-chr2:73845193..73847014,2	MCF-7	breast:

Extended variants
information (count: 171 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs10168931	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169213	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169714	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170786	0.91[EUR][1000 genomes]
rs10170849	0.82[EUR][1000 genomes]
rs10173534	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178409	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10178678	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179134	1.00[ASN][1000 genomes]
rs10181563	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183818	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185080	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187416	0.81[EUR][1000 genomes]
rs10190219	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193972	0.81[EUR][1000 genomes]
rs10197409	0.89[EUR][1000 genomes]
rs10197755	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198549	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199224	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206899	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10207220	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207264	0.81[EUR][1000 genomes]
rs10209517	0.95[EUR][1000 genomes]
rs10469966	1.00[ASN][1000 genomes]
rs10496192	1.00[ASN][1000 genomes]
rs10496193	0.86[EUR][1000 genomes]
rs1052162	0.94[EUR][1000 genomes]
rs11126404	0.83[EUR][1000 genomes]
rs1114380	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674602	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675958	1.00[ASN][1000 genomes]
rs11676385	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679594	1.00[ASN][1000 genomes]
rs11680965	1.00[ASN][1000 genomes]
rs11686019	0.83[EUR][1000 genomes]
rs11686541	1.00[ASN][1000 genomes]
rs11689164	1.00[ASN][1000 genomes]
rs11689588	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693586	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693588	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884776	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11893881	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899740	1.00[ASN][1000 genomes]
rs11899902	1.00[ASN][1000 genomes]
rs11903916	0.91[EUR][1000 genomes]
rs13383871	1.00[ASN][1000 genomes]
rs13384756	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384952	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385564	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391258	0.86[EUR][1000 genomes]
rs13391552	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392691	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392872	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398956	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13400985	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409366	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409668	0.82[EUR][1000 genomes]
rs13410232	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411311	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13421462	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427832	0.95[EUR][1000 genomes]
rs13428235	1.00[ASN][1000 genomes]
rs13431267	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431529	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432605	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13538	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403284	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589576	1.00[ASN][1000 genomes]
rs17009149	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009159	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17349321	1.00[ASN][1000 genomes]
rs2056486	0.81[EUR][1000 genomes]
rs2140195	0.80[EUR][1000 genomes]
rs2421552	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421555	0.91[EUR][1000 genomes]
rs2421577	0.95[EUR][1000 genomes]
rs2567598	1.00[ASN][1000 genomes]
rs2567601	1.00[ASN][1000 genomes]
rs2567602	1.00[ASN][1000 genomes]
rs2567603	1.00[ASN][1000 genomes]
rs28879089	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.81[EUR][1000 genomes]
rs4547554	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56154726	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58603761	0.81[EUR][1000 genomes]
rs62149774	1.00[ASN][1000 genomes]
rs62149777	1.00[ASN][1000 genomes]
rs62149781	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149782	1.00[ASN][1000 genomes]
rs62149804	1.00[ASN][1000 genomes]
rs62151646	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62151652	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153182	1.00[ASN][1000 genomes]
rs62153183	1.00[ASN][1000 genomes]
rs6546845	0.86[EUR][1000 genomes]
rs6546847	0.89[EUR][1000 genomes]
rs6546849	0.94[EUR][1000 genomes]
rs6546850	0.94[EUR][1000 genomes]
rs6546851	0.94[EUR][1000 genomes]
rs6546852	0.94[EUR][1000 genomes]
rs6546853	0.94[EUR][1000 genomes]
rs6546854	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546856	0.92[EUR][1000 genomes]
rs6546857	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546858	0.95[EUR][1000 genomes]
rs6546859	0.95[EUR][1000 genomes]
rs6546860	0.95[EUR][1000 genomes]
rs6546861	0.86[EUR][1000 genomes]
rs6704782	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705489	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705977	0.86[EUR][1000 genomes]
rs6708766	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710438	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711001	0.85[EUR][1000 genomes]
rs6711033	0.82[EUR][1000 genomes]
rs6718843	0.85[EUR][1000 genomes]
rs6719753	0.80[EUR][1000 genomes]
rs6723247	0.95[EUR][1000 genomes]
rs6726694	0.95[EUR][1000 genomes]
rs6735946	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736866	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744398	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745368	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745480	0.95[EUR][1000 genomes]
rs6753344	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755217	1.00[ASN][1000 genomes]
rs6755241	1.00[ASN][1000 genomes]
rs6756885	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759452	1.00[ASN][1000 genomes]
rs73947808	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7424690	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558944	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564890	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566364	0.95[EUR][1000 genomes]
rs7566385	0.82[EUR][1000 genomes]
rs7567585	0.81[EUR][1000 genomes]
rs7572722	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576245	0.94[EUR][1000 genomes]
rs7580750	0.89[EUR][1000 genomes]
rs7580825	1.00[ASN][1000 genomes]
rs7582051	1.00[ASN][1000 genomes]
rs7582606	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583255	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587577	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588169	0.81[EUR][1000 genomes]
rs7594511	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598396	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598419	0.93[EUR][1000 genomes]
rs7602980	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603647	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604682	0.89[EUR][1000 genomes]
rs7607014	0.81[EUR][1000 genomes]
rs7607892	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309473	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9653557	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749859	0.91[EUR][1000 genomes]
rs9750915	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
5	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv874268	chr2:73837751-73907696	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv874269	chr2:73837751-73914019	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv874270	chr2:73837751-73916672	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1015036	chr2:73840055-73891004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1006235	chr2:73840055-73896603	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1006033	chr2:73840055-73900856	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7596773	ALMS1P	cis	Nerve Tibial	GTEx
rs7596773	ALMS1P	cis	Thyroid	GTEx
rs7596773	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs7596773	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73830600-73847600	Weak transcription	Spleen	Spleen
2	chr2:73830600-73854800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:73836400-73852600	Weak transcription	Ovary	ovary
4	chr2:73838400-73852600	Weak transcription	Right Ventricle	heart
5	chr2:73838600-73847400	Weak transcription	Brain Angular Gyrus	brain
6	chr2:73838600-73852600	Weak transcription	Pancreas	Pancrea
7	chr2:73838800-73846600	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:73838800-73849600	Weak transcription	Brain Germinal Matrix	brain
9	chr2:73839600-73846400	Weak transcription	Thymus	Thymus
10	chr2:73842600-73847000	Weak transcription	Primary T cells from cord blood	blood
11	chr2:73842600-73852600	Weak transcription	Left Ventricle	heart
12	chr2:73844000-73846200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:73844000-73854800	Weak transcription	Fetal Brain Female	brain
14	chr2:73844200-73846000	Weak transcription	Brain Anterior Caudate	brain
15	chr2:73844200-73848800	Weak transcription	Aorta	Aorta

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