Variant report

Variant	rs4653920
Chromosome Location	chr1:228375407-228375408
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228362000..228364090-chr1:228375070..228376990,2	MCF-7	breast:
2	chr1:228368663..228372025-chr1:228373776..228376708,3	K562	blood:
3	chr1:228369516..228372082-chr1:228373612..228375927,2	K562	blood:
4	chr1:228373990..228375977-chr1:228378218..228380125,2	K562	blood:

Variant related genes	Relation type
ENSG00000181873	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1059778	0.85[EUR][1000 genomes]
rs10753445	0.84[EUR][1000 genomes]
rs10799468	0.82[EUR][1000 genomes]
rs10799469	0.86[AFR][1000 genomes]
rs10916268	0.81[EUR][1000 genomes]
rs10916271	0.85[EUR][1000 genomes]
rs10916277	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12084338	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12097591	0.95[EUR][1000 genomes]
rs12130630	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134624	0.94[EUR][1000 genomes]
rs1411911	0.85[EUR][1000 genomes]
rs1557026	0.96[EUR][1000 genomes]
rs17623766	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17640616	0.86[EUR][1000 genomes]
rs2185544	0.85[EUR][1000 genomes]
rs2298014	0.95[EUR][1000 genomes]
rs2313600	0.95[EUR][1000 genomes]
rs2313602	0.81[EUR][1000 genomes]
rs4653536	0.84[EUR][1000 genomes]
rs4653907	0.93[EUR][1000 genomes]
rs4653915	0.80[EUR][1000 genomes]
rs4653917	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4653919	0.97[EUR][1000 genomes]
rs4653921	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55658545	0.86[EUR][1000 genomes]
rs55873533	0.94[EUR][1000 genomes]
rs61825279	0.82[EUR][1000 genomes]
rs6426492	0.86[EUR][1000 genomes]
rs6657968	0.96[EUR][1000 genomes]
rs6661539	0.86[EUR][1000 genomes]
rs6673893	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6682260	0.97[EUR][1000 genomes]
rs72757811	0.97[EUR][1000 genomes]
rs72757812	0.97[EUR][1000 genomes]
rs72757824	0.96[EUR][1000 genomes]
rs72757827	0.95[EUR][1000 genomes]
rs72757829	0.89[EUR][1000 genomes]
rs7532141	0.84[EUR][1000 genomes]
rs7539762	0.85[AMR][1000 genomes];0.99[EUR][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	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
11	esv1808523	chr1:228359177-228400358	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4653920	IBA57	cis	Whole Blood	GTEx
rs4653920	OBSCN	cis	Esophagus Mucosa	GTEx
rs4653920	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354400-228384600	Weak transcription	Aorta	Aorta
2	chr1:228354600-228382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
4	chr1:228363400-228375800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:228363400-228386400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:228363800-228385200	Weak transcription	Adipose Nuclei	Adipose
7	chr1:228364000-228384800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:228364400-228386600	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:228364400-228388600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:228364600-228386600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:228364800-228375800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:228364800-228385600	Weak transcription	Brain Anterior Caudate	brain
13	chr1:228365000-228377600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:228365000-228379600	Weak transcription	Gastric	stomach
15	chr1:228365000-228380400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:228365200-228386600	Weak transcription	Thymus	Thymus
17	chr1:228365200-228387800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:228365800-228375800	Weak transcription	Fetal Brain Female	brain
19	chr1:228365800-228382600	Weak transcription	Spleen	Spleen
20	chr1:228366000-228386400	Weak transcription	Primary B cells from cord blood	blood
21	chr1:228366800-228379600	Weak transcription	Placenta	Placenta
22	chr1:228366800-228385200	Weak transcription	Ovary	ovary
23	chr1:228366800-228386600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:228366800-228393400	Weak transcription	Right Ventricle	heart
25	chr1:228368600-228376000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:228369600-228376000	Weak transcription	Fetal Intestine Small	intestine
27	chr1:228369600-228379600	Weak transcription	Lung	lung
28	chr1:228369800-228379600	Weak transcription	Psoas Muscle	Psoas
29	chr1:228370000-228378800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:228371200-228386400	Weak transcription	Primary T cells from cord blood	blood
31	chr1:228372000-228377800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:228372400-228379600	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:228373000-228377000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:228373600-228382600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:228373800-228386200	Weak transcription	Fetal Stomach	stomach
36	chr1:228373800-228394000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:228374800-228376800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr1:228374800-228376800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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