Variant report

Variant	rs4653536
Chromosome Location	chr1:228368454-228368455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228186731..228187465-chr1:228367749..228368702,2	MCF-7	breast:
2	chr1:228367725..228372821-chr1:228377689..228380181,6	MCF-7	breast:
3	chr1:228362275..228366557-chr1:228367502..228371326,4	MCF-7	breast:
4	chr1:228351806..228354795-chr1:228367346..228368993,2	MCF-7	breast:
5	chr1:228368050..228370478-chr1:228645096..228646791,2	K562	blood:
6	chr1:228270273..228272370-chr1:228367891..228370127,2	K562	blood:

Variant related genes	Relation type
ENSG00000196890	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1059778	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753445	0.94[EUR][1000 genomes]
rs10799468	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10799469	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10799471	0.84[EUR][1000 genomes]
rs10916265	0.82[EUR][1000 genomes]
rs10916268	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916271	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11584385	0.81[EUR][1000 genomes]
rs11799681	0.84[EUR][1000 genomes]
rs11804508	0.85[EUR][1000 genomes]
rs12024649	0.84[EUR][1000 genomes]
rs12084338	0.84[EUR][1000 genomes]
rs12130630	0.85[EUR][1000 genomes]
rs12134624	0.83[EUR][1000 genomes]
rs12564763	0.90[EUR][1000 genomes]
rs12726781	0.85[EUR][1000 genomes]
rs12745416	0.85[EUR][1000 genomes]
rs1331303	0.81[EUR][1000 genomes]
rs1411910	0.81[EUR][1000 genomes]
rs1557026	0.80[EUR][1000 genomes]
rs1620111	0.85[EUR][1000 genomes]
rs1629290	0.81[EUR][1000 genomes]
rs1629294	0.82[EUR][1000 genomes]
rs1757129	0.81[EUR][1000 genomes]
rs1757132	0.81[EUR][1000 genomes]
rs1757133	0.82[EUR][1000 genomes]
rs1757138	0.80[EUR][1000 genomes]
rs1757139	0.81[EUR][1000 genomes]
rs1757140	0.82[EUR][1000 genomes]
rs1757141	0.82[EUR][1000 genomes]
rs1757144	0.81[EUR][1000 genomes]
rs1757145	0.83[EUR][1000 genomes]
rs1757147	0.82[EUR][1000 genomes]
rs1757148	0.82[EUR][1000 genomes]
rs1757149	0.82[EUR][1000 genomes]
rs1757150	0.82[EUR][1000 genomes]
rs1757151	0.82[EUR][1000 genomes]
rs1757152	0.81[EUR][1000 genomes]
rs1757155	0.81[EUR][1000 genomes]
rs1757156	0.82[EUR][1000 genomes]
rs1757158	0.83[EUR][1000 genomes]
rs1771459	0.81[EUR][1000 genomes]
rs1771460	0.81[EUR][1000 genomes]
rs1771461	0.81[EUR][1000 genomes]
rs1771462	0.81[EUR][1000 genomes]
rs1771467	0.81[EUR][1000 genomes]
rs1771469	0.81[EUR][1000 genomes]
rs1771470	0.81[EUR][1000 genomes]
rs1771471	0.81[EUR][1000 genomes]
rs1771472	0.82[EUR][1000 genomes]
rs1771474	0.82[EUR][1000 genomes]
rs1771476	0.82[EUR][1000 genomes]
rs1771477	0.82[EUR][1000 genomes]
rs1771478	0.82[EUR][1000 genomes]
rs1771479	0.82[EUR][1000 genomes]
rs1771482	0.81[EUR][1000 genomes]
rs1771483	0.82[EUR][1000 genomes]
rs1771484	0.83[EUR][1000 genomes]
rs1771485	0.83[EUR][1000 genomes]
rs1771487	0.84[EUR][1000 genomes]
rs2185544	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298014	0.84[EUR][1000 genomes]
rs2313601	0.85[EUR][1000 genomes]
rs2313602	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2776845	0.82[EUR][1000 genomes]
rs2776853	0.85[EUR][1000 genomes]
rs2776855	0.81[EUR][1000 genomes]
rs2776856	0.80[EUR][1000 genomes]
rs2792984	0.83[EUR][1000 genomes]
rs2872538	0.81[EUR][1000 genomes]
rs3121191	0.83[EUR][1000 genomes]
rs3121192	0.84[EUR][1000 genomes]
rs3795777	0.81[EUR][1000 genomes]
rs4653543	0.81[EUR][1000 genomes]
rs4653907	0.83[EUR][1000 genomes]
rs4653915	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653917	0.84[EUR][1000 genomes]
rs4653919	0.83[EUR][1000 genomes]
rs4653920	0.84[EUR][1000 genomes]
rs4653921	0.83[EUR][1000 genomes]
rs4653931	0.82[EUR][1000 genomes]
rs55873533	0.83[EUR][1000 genomes]
rs55971985	0.85[EUR][1000 genomes]
rs56112646	0.81[EUR][1000 genomes]
rs61827540	0.82[EUR][1000 genomes]
rs6657968	0.80[EUR][1000 genomes]
rs6673893	0.83[EUR][1000 genomes]
rs6682260	0.85[EUR][1000 genomes]
rs72757811	0.85[EUR][1000 genomes]
rs72757812	0.83[EUR][1000 genomes]
rs72757824	0.80[EUR][1000 genomes]
rs7512209	0.92[EUR][1000 genomes]
rs7532924	0.89[EUR][1000 genomes]
rs7537636	0.92[EUR][1000 genomes]
rs7539762	0.83[EUR][1000 genomes]
rs947087	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
12	nsv873262	chr1:228340653-228371098	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653536	OBSCN	cis	Esophagus Mucosa	GTEx
rs4653536	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354400-228384600	Weak transcription	Aorta	Aorta
2	chr1:228354600-228370400	Weak transcription	Right Atrium	heart
3	chr1:228354600-228382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
5	chr1:228354800-228370800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:228354800-228371200	Weak transcription	HSMMtube	muscle
7	chr1:228354800-228373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:228355000-228370600	Weak transcription	HepG2	liver
9	chr1:228355000-228372400	Weak transcription	Stomach Mucosa	stomach
10	chr1:228355000-228373200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:228355000-228373200	Weak transcription	Hela-S3	cervix
12	chr1:228362600-228368600	Weak transcription	Psoas Muscle	Psoas
13	chr1:228363200-228373200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:228363200-228373200	Weak transcription	Fetal Thymus	thymus
15	chr1:228363400-228375000	Weak transcription	Esophagus	oesophagus
16	chr1:228363400-228375800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:228363400-228386400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:228363600-228373200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:228363600-228374800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:228363800-228368800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:228363800-228373400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:228363800-228385200	Weak transcription	Adipose Nuclei	Adipose
23	chr1:228364000-228369200	Weak transcription	Colonic Mucosa	Colon
24	chr1:228364000-228371600	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:228364000-228373000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:228364000-228373000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:228364000-228373200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:228364000-228384800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:228364200-228371800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:228364400-228368800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:228364400-228386600	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:228364400-228388600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:228364600-228369000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:228364600-228373000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:228364600-228386600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:228364800-228370800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:228364800-228373400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:228364800-228375800	Weak transcription	Brain Germinal Matrix	brain
39	chr1:228364800-228385600	Weak transcription	Brain Anterior Caudate	brain
40	chr1:228365000-228371600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:228365000-228373000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:228365000-228377600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:228365000-228379600	Weak transcription	Gastric	stomach
44	chr1:228365000-228380400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:228365200-228369000	Weak transcription	Lung	lung
46	chr1:228365200-228375400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:228365200-228386600	Weak transcription	Thymus	Thymus
48	chr1:228365200-228387800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:228365600-228370600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:228365800-228375800	Weak transcription	Fetal Brain Female	brain

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