Variant report

Variant	rs6546859
Chromosome Location	chr2:73842055-73842056
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 169 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10169213	0.89[EUR][1000 genomes]
rs10169714	0.89[EUR][1000 genomes]
rs10170786	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173534	0.91[EUR][1000 genomes]
rs10178409	0.86[EUR][1000 genomes]
rs10178678	0.83[EUR][1000 genomes]
rs10181563	0.84[EUR][1000 genomes]
rs10183818	0.80[EUR][1000 genomes]
rs10184268	1.00[ASN][1000 genomes]
rs10185080	0.88[EUR][1000 genomes]
rs10186501	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.80[EUR][1000 genomes]
rs10187416	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189574	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	0.94[CEU][hapmap]
rs10193972	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195357	1.00[ASN][1000 genomes]
rs10195358	1.00[ASN][1000 genomes]
rs10197409	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197755	0.88[EUR][1000 genomes]
rs10198549	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10199224	0.82[EUR][1000 genomes]
rs10206899	1.00[CEU][hapmap]
rs10207220	0.89[EUR][1000 genomes]
rs10207264	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209517	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496191	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496192	0.83[CEU][hapmap]
rs10496193	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126404	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114380	0.89[EUR][1000 genomes]
rs11674602	0.81[EUR][1000 genomes]
rs11676385	0.81[EUR][1000 genomes]
rs11686019	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689588	0.86[EUR][1000 genomes]
rs11693586	0.81[EUR][1000 genomes]
rs11693588	0.81[EUR][1000 genomes]
rs11884776	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11893881	0.93[EUR][1000 genomes]
rs11901272	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903916	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384952	0.82[EUR][1000 genomes]
rs13385564	0.80[EUR][1000 genomes]
rs13391258	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391552	0.90[EUR][1000 genomes]
rs13392691	0.82[EUR][1000 genomes]
rs13398956	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs13400985	0.80[EUR][1000 genomes]
rs13409366	0.95[EUR][1000 genomes]
rs13409668	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410232	1.00[CEU][hapmap]
rs13411311	0.81[EUR][1000 genomes]
rs13421462	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs13427832	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431267	0.86[EUR][1000 genomes]
rs13432605	0.91[EUR][1000 genomes]
rs13538	1.00[CEU][hapmap]
rs1403284	0.81[EUR][1000 genomes]
rs1534471	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009149	0.89[EUR][1000 genomes]
rs17009159	0.89[EUR][1000 genomes]
rs1881245	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918863	1.00[ASN][1000 genomes]
rs2056486	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140195	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280506	0.83[YRI][hapmap]
rs2421550	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421552	0.82[EUR][1000 genomes]
rs2421555	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879089	0.90[EUR][1000 genomes]
rs2901438	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2947845	0.84[YRI][hapmap]
rs2948441	0.84[YRI][hapmap]
rs3738848	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500972	0.87[ASN][1000 genomes]
rs4627598	0.84[YRI][hapmap]
rs4852311	0.82[YRI][hapmap]
rs56154726	0.82[EUR][1000 genomes]
rs58603761	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149781	0.87[EUR][1000 genomes]
rs6546835	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546836	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546837	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546839	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546845	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546847	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546849	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546850	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546851	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546852	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546853	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546854	0.94[EUR][1000 genomes]
rs6546856	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546857	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs6546858	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546860	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546861	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704782	0.86[EUR][1000 genomes]
rs6705489	0.94[CEU][hapmap]
rs6705977	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707722	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708766	0.81[EUR][1000 genomes]
rs6710438	0.91[EUR][1000 genomes]
rs6711001	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711033	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6718843	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719753	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723247	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724782	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726694	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735946	0.89[EUR][1000 genomes]
rs6740223	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.89[EUR][1000 genomes]
rs6744273	0.84[YRI][hapmap]
rs6745368	0.91[EUR][1000 genomes]
rs6745480	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756885	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6756987	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759452	0.89[CEU][hapmap]
rs73947808	0.82[EUR][1000 genomes]
rs7424690	0.87[EUR][1000 genomes]
rs7558944	0.91[EUR][1000 genomes]
rs7566364	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566385	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.82[EUR][1000 genomes]
rs7576245	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580750	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582606	0.91[EUR][1000 genomes]
rs7583255	0.89[EUR][1000 genomes]
rs7584575	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585004	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.89[EUR][1000 genomes]
rs7587577	0.94[EUR][1000 genomes]
rs7588169	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	0.94[CEU][hapmap]
rs7596773	0.95[EUR][1000 genomes]
rs7598419	0.89[EUR][1000 genomes]
rs7598946	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	0.80[EUR][1000 genomes]
rs7603647	0.90[EUR][1000 genomes]
rs7604682	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607014	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607892	0.90[EUR][1000 genomes]
rs7607989	0.83[YRI][hapmap]
rs9309473	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9653557	0.89[EUR][1000 genomes]
rs9749859	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750915	0.91[EUR][1000 genomes]
rs9753079	1.00[ASN][1000 genomes]
rs9807961	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	nsv963620	chr2:73841121-73844121	Strong transcription Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6546859	ALMS1	cis	normal skin	skin_eQTL
rs6546859	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6546859	ALMS1P	cis	Artery Tibial	GTEx
rs6546859	ALMS1P	cis	Thyroid	GTEx
rs6546859	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73801000-73844000	Weak transcription	Fetal Kidney	kidney
2	chr2:73823000-73844600	Weak transcription	Primary B cells from cord blood	blood
3	chr2:73829400-73845400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:73830400-73843600	Weak transcription	Aorta	Aorta
5	chr2:73830600-73843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:73830600-73847600	Weak transcription	Spleen	Spleen
7	chr2:73830600-73854800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:73831000-73842200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:73836400-73844200	Weak transcription	Adipose Nuclei	Adipose
10	chr2:73836400-73852600	Weak transcription	Ovary	ovary
11	chr2:73837400-73845000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:73838000-73845200	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:73838200-73843200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:73838400-73842200	Weak transcription	Brain Anterior Caudate	brain
15	chr2:73838400-73844200	Weak transcription	Fetal Lung	lung
16	chr2:73838400-73844200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:73838400-73852600	Weak transcription	Right Ventricle	heart
18	chr2:73838600-73842200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr2:73838600-73843800	Weak transcription	Lung	lung
20	chr2:73838600-73845200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:73838600-73845400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:73838600-73847400	Weak transcription	Brain Angular Gyrus	brain
23	chr2:73838600-73852600	Weak transcription	Pancreas	Pancrea
24	chr2:73838800-73842200	Weak transcription	Fetal Intestine Small	intestine
25	chr2:73838800-73843400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:73838800-73845800	Weak transcription	Fetal Stomach	stomach
27	chr2:73838800-73846600	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:73838800-73849600	Weak transcription	Brain Germinal Matrix	brain
29	chr2:73839000-73842200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:73839200-73842400	Weak transcription	Fetal Brain Female	brain
31	chr2:73839200-73844000	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr2:73839600-73845600	Weak transcription	Brain Substantia Nigra	brain
33	chr2:73839600-73846400	Weak transcription	Thymus	Thymus
34	chr2:73840400-73842800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr2:73841200-73842600	Strong transcription	Primary T cells from cord blood	blood
36	chr2:73841600-73843400	Weak transcription	GM12878-XiMat	blood
37	chr2:73841800-73844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:73842000-73842400	Weak transcription	Left Ventricle	heart
39	chr2:73842000-73842800	Strong transcription	Brain Cingulate Gyrus	brain
40	chr2:73842000-73842800	Enhancers	Right Atrium	heart

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