Variant report

Variant	rs1771477
Chromosome Location	chr1:228413929-228413930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:228413818..228415485-chr1:228417665..228419917,2	K562	blood:
2	chr1:228412002..228414034-chr1:228460124..228463067,2	K562	blood:
3	chr1:228413308..228415360-chr1:228448839..228451270,2	K562	blood:
4	chr1:228413127..228415318-chr1:228418110..228419917,2	K562	blood:
5	chr1:228413238..228414858-chr1:228417305..228419421,2	MCF-7	breast:
6	chr1:228407306..228411999-chr1:228412295..228416286,6	K562	blood:
7	chr1:228407306..228411999-chr1:228412295..228415050,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269890	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1059778	0.84[EUR][1000 genomes]
rs10753445	0.84[EUR][1000 genomes]
rs10799468	0.81[EUR][1000 genomes]
rs10799471	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10916268	0.81[EUR][1000 genomes]
rs10916271	0.84[EUR][1000 genomes]
rs11580411	0.85[EUR][1000 genomes]
rs11584385	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11799681	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11804508	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12024649	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12118872	0.83[EUR][1000 genomes]
rs12726781	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12745416	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1331303	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1411910	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1411911	0.85[EUR][1000 genomes]
rs1411913	0.85[EUR][1000 genomes]
rs1620111	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1629290	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1629294	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757129	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1757132	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757133	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1757138	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757139	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757140	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1757141	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1757142	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1757144	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757145	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1757147	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757148	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757149	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757150	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757151	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1757152	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757155	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757156	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757158	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17640616	0.86[EUR][1000 genomes]
rs1771459	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771460	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1771461	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1771462	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1771467	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771468	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1771469	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1771470	0.98[EUR][1000 genomes]
rs1771471	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771472	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771474	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771476	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771478	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771479	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771482	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771483	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771484	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1771485	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771487	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2185544	0.84[EUR][1000 genomes]
rs2313601	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2313602	0.81[EUR][1000 genomes]
rs2776845	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2776853	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2776855	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2776856	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2792984	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2872538	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2989563	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3121188	0.85[EUR][1000 genomes]
rs3121190	0.86[EUR][1000 genomes]
rs3121191	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3121192	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3795777	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3795782	0.84[EUR][1000 genomes]
rs4653536	0.82[EUR][1000 genomes]
rs4653543	0.96[EUR][1000 genomes]
rs4653545	0.93[EUR][1000 genomes]
rs4653931	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653933	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653934	0.84[EUR][1000 genomes]
rs489926	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs491293	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs493945	0.82[EUR][1000 genomes]
rs512406	0.92[EUR][1000 genomes]
rs545313	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs546967	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55658545	0.86[EUR][1000 genomes]
rs55971985	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56112646	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56168609	0.82[EUR][1000 genomes]
rs566640	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61825279	0.82[EUR][1000 genomes]
rs61827540	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6661539	0.86[EUR][1000 genomes]
rs72757829	0.83[EUR][1000 genomes]
rs7525075	0.93[EUR][1000 genomes]
rs7532141	0.83[EUR][1000 genomes]
rs7532924	0.87[EUR][1000 genomes]
rs947087	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1771477	OBSCN	cis	Esophagus Mucosa	GTEx
rs1771477	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228402200-228415200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:228402200-228425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:228402600-228418000	Strong transcription	Primary T cells from cord blood	blood
5	chr1:228403000-228428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:228403200-228418000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:228403400-228415000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:228410000-228416600	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr1:228410200-228414800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
10	chr1:228410400-228415600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:228410600-228416400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:228410800-228416800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:228411000-228415000	Weak transcription	Small Intestine	intestine
14	chr1:228411600-228416000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:228411600-228416800	Strong transcription	Dnd41	blood
16	chr1:228411800-228414200	ZNF genes & repeats	Lung	lung
17	chr1:228411800-228414200	ZNF genes & repeats	Spleen	Spleen
18	chr1:228411800-228415000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:228411800-228416200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:228411800-228416400	Weak transcription	K562	blood
21	chr1:228411800-228417000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:228411800-228420200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:228412000-228414400	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr1:228412000-228416800	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr1:228412200-228414000	ZNF genes & repeats	A549	lung
26	chr1:228412400-228420400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:228412600-228415200	Genic enhancers	Right Ventricle	heart
28	chr1:228412600-228420800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:228412800-228414000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:228412800-228414400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:228412800-228414400	Strong transcription	Fetal Intestine Large	intestine
32	chr1:228412800-228415200	Weak transcription	Colonic Mucosa	Colon
33	chr1:228412800-228416800	Strong transcription	Fetal Thymus	thymus
34	chr1:228413000-228414000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:228413000-228414800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:228413000-228415200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:228413000-228416200	Strong transcription	Thymus	Thymus
38	chr1:228413000-228416800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:228413000-228425600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:228413000-228426000	Weak transcription	Right Atrium	heart
41	chr1:228413000-228428400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:228413000-228428800	Weak transcription	Gastric	stomach
43	chr1:228413200-228414000	Strong transcription	Left Ventricle	heart
44	chr1:228413200-228414200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr1:228413200-228414200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:228413200-228414400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:228413200-228414400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:228413200-228414400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:228413200-228414600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:228413200-228414800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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