Variant report

Variant	rs566640
Chromosome Location	chr1:228449573-228449574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228418003..228421398-chr1:228446860..228450247,3	K562	blood:
2	chr1:228447727..228450051-chr1:228461842..228464291,2	MCF-7	breast:
3	chr1:228449283..228451811-chr1:228461378..228463702,3	K562	blood:
4	chr1:228413308..228415360-chr1:228448839..228451270,2	K562	blood:
5	chr1:228445781..228449688-chr1:228450143..228453415,4	K562	blood:

Variant related genes	Relation type
ENSG00000269890	Chromatin interaction
ENSG00000269934	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10753445	0.80[EUR][1000 genomes]
rs10799471	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11578798	0.91[ASN][1000 genomes]
rs11580411	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11581167	0.91[ASN][1000 genomes]
rs11582927	0.91[ASN][1000 genomes]
rs11584385	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799681	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11804508	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12024649	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118872	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12726781	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12745416	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1331303	0.94[EUR][1000 genomes]
rs1411910	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1411911	0.84[EUR][1000 genomes]
rs1411913	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1620111	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1629290	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1629294	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757129	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757132	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757133	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757138	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757139	0.94[EUR][1000 genomes]
rs1757140	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757141	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757142	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1757144	0.92[EUR][1000 genomes]
rs1757145	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757147	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1757148	0.92[EUR][1000 genomes]
rs1757149	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757150	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757151	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757152	0.92[EUR][1000 genomes]
rs1757155	0.92[EUR][1000 genomes]
rs1757156	0.93[EUR][1000 genomes]
rs1757158	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17640616	0.83[EUR][1000 genomes]
rs1771459	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1771460	0.93[EUR][1000 genomes]
rs1771461	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1771462	0.93[EUR][1000 genomes]
rs1771467	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1771468	0.92[EUR][1000 genomes]
rs1771469	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1771470	0.92[EUR][1000 genomes]
rs1771471	0.92[EUR][1000 genomes]
rs1771472	0.92[EUR][1000 genomes]
rs1771474	0.92[EUR][1000 genomes]
rs1771476	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1771477	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1771478	0.93[EUR][1000 genomes]
rs1771479	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1771482	0.92[EUR][1000 genomes]
rs1771483	0.93[EUR][1000 genomes]
rs1771484	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771485	0.92[EUR][1000 genomes]
rs1771487	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2313601	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2776845	0.93[EUR][1000 genomes]
rs2776853	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2776855	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2776856	0.93[EUR][1000 genomes]
rs2792984	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2872538	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2989563	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3121190	0.83[EUR][1000 genomes]
rs3121191	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3121192	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3795777	0.91[EUR][1000 genomes]
rs3795782	0.91[EUR][1000 genomes]
rs3795795	0.91[ASN][1000 genomes]
rs3795801	0.91[ASN][1000 genomes]
rs45473794	0.83[ASN][1000 genomes]
rs4653543	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653545	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653549	0.91[ASN][1000 genomes]
rs4653931	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653933	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653934	0.91[EUR][1000 genomes]
rs4653935	0.91[ASN][1000 genomes]
rs4653936	0.91[ASN][1000 genomes]
rs4653941	0.91[ASN][1000 genomes]
rs474735	0.92[ASN][1000 genomes]
rs489926	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs493945	0.85[EUR][1000 genomes]
rs504474	0.92[ASN][1000 genomes]
rs512406	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs535329	0.92[ASN][1000 genomes]
rs545313	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs546967	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55658545	0.83[EUR][1000 genomes]
rs55971985	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56021350	0.91[ASN][1000 genomes]
rs56112646	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56168609	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61825279	0.87[EUR][1000 genomes]
rs61825301	0.91[ASN][1000 genomes]
rs61825302	0.91[ASN][1000 genomes]
rs61825308	0.91[ASN][1000 genomes]
rs61827540	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6661539	0.80[EUR][1000 genomes]
rs72757829	0.80[EUR][1000 genomes]
rs7525075	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7532141	0.84[EUR][1000 genomes]
rs7532924	0.81[EUR][1000 genomes]
rs936884	0.92[ASN][1000 genomes]
rs947087	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv945350	chr1:228448721-228451969	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs566640	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs566640	OBSCN	cis	Esophagus Mucosa	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	chr1:228435200-228449600	Strong transcription	Primary T cells from cord blood	blood
5	chr1:228435200-228462800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:228435600-228462600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:228435800-228450200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:228437000-228455600	Weak transcription	Hela-S3	cervix
9	chr1:228438400-228455600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:228441200-228450400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:228443200-228454800	Strong transcription	Left Ventricle	heart
12	chr1:228443400-228449800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:228443600-228462800	Weak transcription	Fetal Kidney	kidney
14	chr1:228444000-228461400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:228444200-228461600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:228444400-228450000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr1:228444600-228450000	ZNF genes & repeats	Dnd41	blood
18	chr1:228444800-228454200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:228444800-228462800	Weak transcription	Fetal Thymus	thymus
20	chr1:228445000-228455800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:228445000-228456400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:228445000-228462200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:228445000-228462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:228445000-228462800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:228445000-228463200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:228446400-228449800	Strong transcription	Fetal Heart	heart
27	chr1:228447200-228449800	Strong transcription	Fetal Lung	lung
28	chr1:228447400-228451400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:228447400-228455800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:228447400-228455800	Weak transcription	Brain Germinal Matrix	brain
31	chr1:228447600-228450400	Weak transcription	Right Atrium	heart
32	chr1:228447600-228451600	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:228447600-228451600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:228447600-228455800	Weak transcription	Lung	lung
35	chr1:228447600-228455800	Weak transcription	Spleen	Spleen
36	chr1:228447600-228463000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:228447800-228454600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:228447800-228455600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:228447800-228455800	Weak transcription	Esophagus	oesophagus
40	chr1:228447800-228460600	Weak transcription	Pancreas	Pancrea
41	chr1:228447800-228461200	Weak transcription	Gastric	stomach
42	chr1:228447800-228462800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:228447800-228463000	Weak transcription	Psoas Muscle	Psoas
44	chr1:228448000-228449800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:228448000-228452600	Weak transcription	Small Intestine	intestine
46	chr1:228448000-228454600	Weak transcription	HSMMtube	muscle
47	chr1:228448000-228455600	Weak transcription	Ovary	ovary
48	chr1:228448200-228449800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:228448200-228450000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:228448200-228450000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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