Variant report

Variant	rs12024649
Chromosome Location	chr1:228398777-228398778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228398723-228399454	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228397487..228399234-chr1:228400392..228402021,2	K562	blood:

Variant related genes	Relation type
OBSCN	TF binding region
ENSG00000162913	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1059778	0.86[EUR][1000 genomes]
rs10753445	0.87[EUR][1000 genomes]
rs10799468	0.83[EUR][1000 genomes]
rs10799469	0.80[EUR][1000 genomes]
rs10799471	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916268	0.84[EUR][1000 genomes]
rs10916271	0.86[EUR][1000 genomes]
rs11580411	0.82[EUR][1000 genomes]
rs11584385	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11799681	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804508	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118872	0.81[EUR][1000 genomes]
rs12726781	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745416	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331303	0.93[EUR][1000 genomes]
rs1411910	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1411911	0.82[EUR][1000 genomes]
rs1411913	0.82[EUR][1000 genomes]
rs1620111	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629290	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1629294	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757129	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757132	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757133	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757138	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757139	0.93[EUR][1000 genomes]
rs1757140	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757141	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757142	0.89[EUR][1000 genomes]
rs1757144	0.93[EUR][1000 genomes]
rs1757145	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1757147	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757148	0.94[EUR][1000 genomes]
rs1757149	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757150	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757151	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1757152	0.93[EUR][1000 genomes]
rs1757153	0.87[ASN][1000 genomes]
rs1757155	0.93[EUR][1000 genomes]
rs1757156	0.94[EUR][1000 genomes]
rs1757158	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17640616	0.83[EUR][1000 genomes]
rs1771459	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1771460	0.92[EUR][1000 genomes]
rs1771461	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771462	0.93[EUR][1000 genomes]
rs1771467	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1771468	0.92[EUR][1000 genomes]
rs1771469	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1771470	0.93[EUR][1000 genomes]
rs1771471	0.93[EUR][1000 genomes]
rs1771472	0.94[EUR][1000 genomes]
rs1771474	0.94[EUR][1000 genomes]
rs1771476	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771477	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771478	0.94[EUR][1000 genomes]
rs1771479	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771482	0.93[EUR][1000 genomes]
rs1771483	0.94[EUR][1000 genomes]
rs1771484	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1771485	0.95[EUR][1000 genomes]
rs1771487	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185544	0.87[EUR][1000 genomes]
rs2313601	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2313602	0.84[EUR][1000 genomes]
rs2776845	0.94[EUR][1000 genomes]
rs2776853	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2776855	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2776856	0.92[EUR][1000 genomes]
rs2792984	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2872538	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2989563	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3121188	0.85[EUR][1000 genomes]
rs3121190	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3121191	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121192	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3795777	0.93[EUR][1000 genomes]
rs3795782	0.82[EUR][1000 genomes]
rs4653536	0.84[EUR][1000 genomes]
rs4653543	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653545	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653915	0.82[EUR][1000 genomes]
rs4653931	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653933	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653934	0.82[EUR][1000 genomes]
rs489926	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs491293	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs512406	0.90[EUR][1000 genomes]
rs545313	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs546967	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55658545	0.83[EUR][1000 genomes]
rs55971985	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56112646	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56168609	0.80[EUR][1000 genomes]
rs566640	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61827540	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6661539	0.82[EUR][1000 genomes]
rs72757829	0.85[EUR][1000 genomes]
rs7512209	0.81[EUR][1000 genomes]
rs7525075	0.91[EUR][1000 genomes]
rs7532141	0.81[EUR][1000 genomes]
rs7532924	0.90[EUR][1000 genomes]
rs7537636	0.81[EUR][1000 genomes]
rs947087	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
12	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	esv3419574	chr1:228397729-228402327	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
14	esv3397989	chr1:228398279-228402677	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12024649	OBSCN	cis	Esophagus Mucosa	GTEx
rs12024649	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228394600-228400200	Weak transcription	Fetal Lung	lung
2	chr1:228395600-228399400	Weak transcription	Lung	lung
3	chr1:228395600-228400200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:228395800-228405200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
5	chr1:228396200-228398800	Weak transcription	Fetal Intestine Small	intestine
6	chr1:228396200-228400200	Weak transcription	Pancreas	Pancrea
7	chr1:228396400-228399000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:228397000-228400400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:228397200-228399000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:228397200-228401000	Enhancers	Fetal Heart	heart
11	chr1:228397600-228400200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:228397800-228399000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr1:228397800-228399400	Enhancers	Hela-S3	cervix
14	chr1:228397800-228400800	Weak transcription	HSMMtube	muscle
15	chr1:228398200-228399000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr1:228398200-228399400	Weak transcription	Esophagus	oesophagus
17	chr1:228398200-228400400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:228398400-228398800	Flanking Active TSS	Psoas Muscle	Psoas
19	chr1:228398400-228398800	Weak transcription	Spleen	Spleen
20	chr1:228398400-228399200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr1:228398400-228399400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:228398400-228400200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:228398400-228400200	Weak transcription	Right Atrium	heart
24	chr1:228398400-228400400	Weak transcription	A549	lung
25	chr1:228398400-228400400	Weak transcription	HSMM	muscle
26	chr1:228398600-228398800	Flanking Active TSS	Left Ventricle	heart
27	chr1:228398600-228399000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:228398600-228399000	Active TSS	Brain Anterior Caudate	brain
29	chr1:228398600-228399000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr1:228398600-228399000	Transcr. at gene 5' and 3'	Right Ventricle	heart

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