Variant report

Variant	rs512406
Chromosome Location	chr1:228452334-228452335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228449665..228453244-chr1:228453932..228455890,3	K562	blood:
2	chr1:228451031..228452706-chr1:228468801..228471254,2	K562	blood:
3	chr1:228451473..228454587-chr1:228643245..228646979,3	K562	blood:
4	chr1:228445781..228449688-chr1:228450143..228453415,4	K562	blood:
5	chr1:228418825..228420344-chr1:228451196..228452824,2	K562	blood:

Variant related genes	Relation type
ENSG00000181218	Chromatin interaction
ENSG00000196890	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10753445	0.80[EUR][1000 genomes]
rs10799471	0.90[EUR][1000 genomes]
rs11580411	0.92[EUR][1000 genomes]
rs11584385	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11799681	0.89[EUR][1000 genomes]
rs11804508	0.91[EUR][1000 genomes]
rs12024649	0.90[EUR][1000 genomes]
rs12118872	0.90[EUR][1000 genomes]
rs12726781	0.91[EUR][1000 genomes]
rs12745416	0.91[EUR][1000 genomes]
rs1331303	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1411910	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1411911	0.84[EUR][1000 genomes]
rs1411913	0.82[EUR][1000 genomes]
rs1620111	0.91[EUR][1000 genomes]
rs1629290	0.92[EUR][1000 genomes]
rs1629294	0.92[EUR][1000 genomes]
rs1757129	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1757132	0.93[EUR][1000 genomes]
rs1757133	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1757138	0.92[EUR][1000 genomes]
rs1757139	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757140	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1757141	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1757142	0.88[EUR][1000 genomes]
rs1757144	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757145	0.94[EUR][1000 genomes]
rs1757147	0.92[EUR][1000 genomes]
rs1757148	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757149	0.92[EUR][1000 genomes]
rs1757150	0.92[EUR][1000 genomes]
rs1757151	0.93[EUR][1000 genomes]
rs1757152	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1757155	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1757156	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757158	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17640616	0.83[EUR][1000 genomes]
rs1771459	0.93[EUR][1000 genomes]
rs1771460	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1771461	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1771462	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1771467	0.93[EUR][1000 genomes]
rs1771468	0.92[EUR][1000 genomes]
rs1771469	0.93[EUR][1000 genomes]
rs1771470	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1771471	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1771472	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1771474	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1771476	0.92[EUR][1000 genomes]
rs1771477	0.92[EUR][1000 genomes]
rs1771478	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1771479	0.92[EUR][1000 genomes]
rs1771482	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1771483	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1771484	0.94[EUR][1000 genomes]
rs1771485	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1771487	0.88[EUR][1000 genomes]
rs2313601	0.91[EUR][1000 genomes]
rs2776845	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2776853	0.91[EUR][1000 genomes]
rs2776855	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2776856	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2792984	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2872538	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2989563	0.82[EUR][1000 genomes]
rs3121190	0.83[EUR][1000 genomes]
rs3121191	0.87[EUR][1000 genomes]
rs3121192	0.89[EUR][1000 genomes]
rs3795777	0.90[EUR][1000 genomes]
rs3795782	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795797	0.85[ASN][1000 genomes]
rs4653543	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653545	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653547	0.85[ASN][1000 genomes]
rs4653931	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653933	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653934	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs489926	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs491293	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs493945	0.85[EUR][1000 genomes]
rs545313	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs546967	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55658545	0.83[EUR][1000 genomes]
rs55971985	0.91[EUR][1000 genomes]
rs56112646	0.93[EUR][1000 genomes]
rs56168609	0.89[EUR][1000 genomes]
rs566640	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61825279	0.87[EUR][1000 genomes]
rs61825307	0.85[ASN][1000 genomes]
rs61827540	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6661539	0.80[EUR][1000 genomes]
rs72757829	0.81[EUR][1000 genomes]
rs7525075	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532141	0.85[EUR][1000 genomes]
rs7532924	0.81[EUR][1000 genomes]
rs876180	0.85[ASN][1000 genomes]
rs947087	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
9	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
10	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
11	nsv873264	chr1:228423647-228543800	Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv520340	chr1:228423936-228456147	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv873265	chr1:228434395-228525008	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats 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	21 gene(s)	inside rSNPs	diseases
14	nsv873266	chr1:228434395-228537942	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
16	nsv873268	chr1:228442663-228537942	Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv873269	chr1:228442663-228543800	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
19	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
20	nsv873271	chr1:228450868-228470995	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv873272	chr1:228450868-228538968	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
22	nsv873273	chr1:228450868-228556788	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
23	nsv873274	chr1:228450868-228585837	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs512406	OBSCN	cis	Esophagus Mucosa	GTEx
rs512406	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228434600-228455400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:228434800-228460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:228434800-228462400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:228435200-228462800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:228435600-228462600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:228437000-228455600	Weak transcription	Hela-S3	cervix
7	chr1:228438400-228455600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:228443200-228454800	Strong transcription	Left Ventricle	heart
9	chr1:228443600-228462800	Weak transcription	Fetal Kidney	kidney
10	chr1:228444000-228461400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:228444200-228461600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:228444800-228454200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:228444800-228462800	Weak transcription	Fetal Thymus	thymus
14	chr1:228445000-228455800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:228445000-228456400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:228445000-228462200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:228445000-228462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:228445000-228462800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:228445000-228463200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:228447400-228455800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:228447400-228455800	Weak transcription	Brain Germinal Matrix	brain
22	chr1:228447600-228455800	Weak transcription	Lung	lung
23	chr1:228447600-228455800	Weak transcription	Spleen	Spleen
24	chr1:228447600-228463000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:228447800-228454600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:228447800-228455600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:228447800-228455800	Weak transcription	Esophagus	oesophagus
28	chr1:228447800-228460600	Weak transcription	Pancreas	Pancrea
29	chr1:228447800-228461200	Weak transcription	Gastric	stomach
30	chr1:228447800-228462800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:228447800-228463000	Weak transcription	Psoas Muscle	Psoas
32	chr1:228448000-228452600	Weak transcription	Small Intestine	intestine
33	chr1:228448000-228454600	Weak transcription	HSMMtube	muscle
34	chr1:228448000-228455600	Weak transcription	Ovary	ovary
35	chr1:228448200-228455800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:228449000-228462600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:228449200-228459400	Weak transcription	Thymus	Thymus
38	chr1:228449200-228462800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:228449400-228455600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:228449800-228454400	Weak transcription	Fetal Heart	heart
41	chr1:228449800-228455600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:228449800-228459800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:228449800-228462600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:228450000-228453800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:228450000-228455000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:228450000-228462800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:228450000-228462800	Weak transcription	Brain Anterior Caudate	brain
48	chr1:228450000-228463000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:228450200-228452400	Weak transcription	Primary T cells from cord blood	blood
50	chr1:228450200-228462000	Weak transcription	Fetal Lung	lung

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