Variant report

Variant	rs55971985
Chromosome Location	chr1:228399766-228399767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF3	chr1:228399535-228399773	GM12878	blood:	n/a	n/a
2	MAX	chr1:228399607-228402252	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr1:228399563-228400691	H1-hESC	embryonic stem cell:	n/a	n/a
4	BACH1	chr1:228399752-228400928	H1-hESC	embryonic stem cell:	n/a	n/a
5	GABPA	chr1:228399617-228400472	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr1:228399552-228400695	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr1:228399633-228400711	H1-hESC	embryonic stem cell:	n/a	chr1:228400690-228400699

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228399534..228402324-chr1:228461653..228463776,2	MCF-7	breast:
2	chr1:228399724..228401498-chr1:228644939..228647172,2	MCF-7	breast:
3	chr1:228399573..228401373-chr1:228480199..228482605,2	K562	blood:
4	chr1:228399084..228400867-chr1:228463770..228467227,3	K562	blood:

No data

Variant related genes	Relation type
OBSCN	TF binding region
ENSG00000181218	Chromatin interaction
ENSG00000269890	Chromatin interaction
ENSG00000269934	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000154358	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1059778	0.87[EUR][1000 genomes]
rs10753445	0.88[EUR][1000 genomes]
rs10799468	0.84[EUR][1000 genomes]
rs10799469	0.81[EUR][1000 genomes]
rs10799471	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916268	0.85[EUR][1000 genomes]
rs10916271	0.87[EUR][1000 genomes]
rs11580411	0.83[EUR][1000 genomes]
rs11584385	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11799681	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11804508	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12024649	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12118872	0.82[EUR][1000 genomes]
rs12726781	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12745416	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1331303	0.94[EUR][1000 genomes]
rs1411910	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1411911	0.83[EUR][1000 genomes]
rs1411913	0.83[EUR][1000 genomes]
rs1620111	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1629290	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1629294	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1757129	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1757132	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757133	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1757138	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757139	0.94[EUR][1000 genomes]
rs1757140	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1757141	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1757142	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1757144	0.94[EUR][1000 genomes]
rs1757145	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757147	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1757148	0.95[EUR][1000 genomes]
rs1757149	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1757150	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1757151	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757152	0.94[EUR][1000 genomes]
rs1757153	0.83[ASN][1000 genomes]
rs1757155	0.94[EUR][1000 genomes]
rs1757156	0.95[EUR][1000 genomes]
rs1757158	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17640616	0.84[EUR][1000 genomes]
rs1771459	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771460	0.93[EUR][1000 genomes]
rs1771461	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1771462	0.94[EUR][1000 genomes]
rs1771467	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771468	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1771469	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1771470	0.94[EUR][1000 genomes]
rs1771471	0.94[EUR][1000 genomes]
rs1771472	0.95[EUR][1000 genomes]
rs1771474	0.95[EUR][1000 genomes]
rs1771476	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1771477	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1771478	0.95[EUR][1000 genomes]
rs1771479	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1771482	0.94[EUR][1000 genomes]
rs1771483	0.95[EUR][1000 genomes]
rs1771484	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1771485	0.96[EUR][1000 genomes]
rs1771487	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2185544	0.88[EUR][1000 genomes]
rs2313601	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2313602	0.85[EUR][1000 genomes]
rs2776845	0.95[EUR][1000 genomes]
rs2776853	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2776855	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2776856	0.93[EUR][1000 genomes]
rs2792984	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2872538	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2989563	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3121188	0.86[EUR][1000 genomes]
rs3121190	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3121191	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3121192	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3795777	0.94[EUR][1000 genomes]
rs3795782	0.83[EUR][1000 genomes]
rs4653536	0.85[EUR][1000 genomes]
rs4653543	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653545	0.91[EUR][1000 genomes]
rs4653915	0.83[EUR][1000 genomes]
rs4653931	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4653933	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653934	0.83[EUR][1000 genomes]
rs489926	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs491293	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs512406	0.91[EUR][1000 genomes]
rs545313	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs546967	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55658545	0.84[EUR][1000 genomes]
rs56112646	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56168609	0.81[EUR][1000 genomes]
rs566640	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61825279	0.80[EUR][1000 genomes]
rs61827540	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6661539	0.83[EUR][1000 genomes]
rs72757827	0.80[EUR][1000 genomes]
rs72757829	0.86[EUR][1000 genomes]
rs7512209	0.82[EUR][1000 genomes]
rs7525075	0.92[EUR][1000 genomes]
rs7532141	0.82[EUR][1000 genomes]
rs7532924	0.89[EUR][1000 genomes]
rs7537636	0.82[EUR][1000 genomes]
rs947087	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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
15	esv3361766	chr1:228399154-228401702	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
16	esv3383939	chr1:228399179-228401177	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
17	esv3358379	chr1:228399204-228403102	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55971985	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs55971985	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228394600-228400200	Weak transcription	Fetal Lung	lung
2	chr1:228395600-228400200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:228395800-228405200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
4	chr1:228396200-228400200	Weak transcription	Pancreas	Pancrea
5	chr1:228397000-228400400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:228397200-228401000	Enhancers	Fetal Heart	heart
7	chr1:228397600-228400200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:228397800-228400800	Weak transcription	HSMMtube	muscle
9	chr1:228398200-228400400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:228398400-228400200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:228398400-228400200	Weak transcription	Right Atrium	heart
12	chr1:228398400-228400400	Weak transcription	A549	lung
13	chr1:228398400-228400400	Weak transcription	HSMM	muscle
14	chr1:228398800-228402000	Active TSS	Psoas Muscle	Psoas
15	chr1:228399000-228400000	Genic enhancers	Right Ventricle	heart
16	chr1:228399000-228400200	Weak transcription	Brain Anterior Caudate	brain
17	chr1:228399000-228400200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:228399000-228400600	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
19	chr1:228399400-228399800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:228399400-228400200	Enhancers	Esophagus	oesophagus
21	chr1:228399400-228400200	Weak transcription	Hela-S3	cervix
22	chr1:228399600-228399800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:228399600-228399800	Weak transcription	Lung	lung
24	chr1:228399600-228400200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:228399600-228400200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:228399600-228400200	Weak transcription	Fetal Intestine Small	intestine
27	chr1:228399600-228400800	Genic enhancers	Left Ventricle	heart
28	chr1:228399600-228400800	Enhancers	Spleen	Spleen

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