Variant report

Variant	rs58066823
Chromosome Location	chr1:174293483-174293484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174293187..174295185-chr1:174300416..174302383,2	K562	blood:
2	chr1:174292133..174293963-chr1:174301470..174303626,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs55669124	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55687343	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55833532	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55896504	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56058592	0.91[AMR][1000 genomes]
rs56179605	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56185645	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56234951	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56391203	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58401153	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58831567	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58842085	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58997380	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59102371	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59753012	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60449770	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126804	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126807	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126808	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126812	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126813	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126815	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126817	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126818	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126819	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126820	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126822	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126823	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126824	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126826	0.91[AMR][1000 genomes]
rs74126827	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126828	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128334	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128335	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128338	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128342	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128343	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128349	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128362	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128369	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128371	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128372	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128374	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128384	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128386	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128391	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1008993	chr1:174180019-174331358	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv872553	chr1:174195629-174373379	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	esv1795045	chr1:174273004-174346276	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58066823	RC3H1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174284600-174294600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:174284800-174294400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:174285200-174294800	Weak transcription	Right Ventricle	heart
4	chr1:174285200-174295200	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:174286000-174296400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:174287000-174293800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:174287000-174296600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:174287200-174294600	Weak transcription	Ovary	ovary
9	chr1:174287200-174294800	Weak transcription	Gastric	stomach
10	chr1:174289000-174295400	ZNF genes & repeats	GM12878-XiMat	blood
11	chr1:174290200-174294600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:174290600-174294600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:174290600-174294600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:174290600-174294800	Weak transcription	Lung	lung
15	chr1:174290600-174294800	Weak transcription	Pancreas	Pancrea
16	chr1:174291000-174293800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:174291000-174294600	Weak transcription	Liver	Liver
18	chr1:174291000-174294800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:174291600-174294000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:174291600-174294400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:174291800-174294600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:174291800-174294600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:174291800-174294800	Weak transcription	Fetal Lung	lung
24	chr1:174292000-174294200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:174292000-174294600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:174292000-174294600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:174292000-174294600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:174292000-174294600	Weak transcription	Left Ventricle	heart
29	chr1:174292000-174294800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:174292000-174294800	Weak transcription	Aorta	Aorta
31	chr1:174292200-174294600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr1:174292200-174294600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:174292200-174294600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:174292200-174294600	Weak transcription	NHEK	skin
35	chr1:174292400-174293600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:174292800-174296400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:174293200-174293600	Weak transcription	Primary B cells from cord blood	blood
38	chr1:174293200-174293600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr1:174293200-174295000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:174293400-174294600	Enhancers	Primary B cells from peripheral blood	blood

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