Variant report

Variant	rs1771470
Chromosome Location	chr1:228417465-228417466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228416742..228420360-chr1:228423118..228426158,4	K562	blood:
2	chr1:228413238..228414858-chr1:228417305..228419421,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1059778	0.83[EUR][1000 genomes]
rs10753445	0.83[EUR][1000 genomes]
rs10799471	0.92[EUR][1000 genomes]
rs10916268	0.80[EUR][1000 genomes]
rs10916271	0.83[EUR][1000 genomes]
rs11580411	0.84[EUR][1000 genomes]
rs11584385	0.96[EUR][1000 genomes]
rs11799681	0.92[EUR][1000 genomes]
rs11804508	0.94[EUR][1000 genomes]
rs12024649	0.93[EUR][1000 genomes]
rs12118872	0.83[EUR][1000 genomes]
rs12726781	0.94[EUR][1000 genomes]
rs12745416	0.94[EUR][1000 genomes]
rs1331303	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1411910	0.96[EUR][1000 genomes]
rs1411911	0.84[EUR][1000 genomes]
rs1411913	0.86[EUR][1000 genomes]
rs1620111	0.94[EUR][1000 genomes]
rs1629290	0.97[EUR][1000 genomes]
rs1629294	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757129	0.96[EUR][1000 genomes]
rs1757132	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1757133	0.97[EUR][1000 genomes]
rs1757138	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1757139	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1757140	0.97[EUR][1000 genomes]
rs1757141	0.97[EUR][1000 genomes]
rs1757142	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757144	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1757145	0.97[EUR][1000 genomes]
rs1757147	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1757148	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1757149	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1757150	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1757151	0.96[EUR][1000 genomes]
rs1757152	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1757155	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1757156	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1757158	0.97[EUR][1000 genomes]
rs17640616	0.84[EUR][1000 genomes]
rs1771459	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771460	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1771461	0.96[EUR][1000 genomes]
rs1771462	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1771467	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771468	0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771469	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771471	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1771472	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1771474	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1771476	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1771477	0.98[EUR][1000 genomes]
rs1771478	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1771479	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1771482	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1771483	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1771484	0.97[EUR][1000 genomes]
rs1771485	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1771487	0.91[EUR][1000 genomes]
rs2185544	0.83[EUR][1000 genomes]
rs2313601	0.94[EUR][1000 genomes]
rs2313602	0.80[EUR][1000 genomes]
rs2776845	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2776853	0.93[EUR][1000 genomes]
rs2776855	0.95[EUR][1000 genomes]
rs2776856	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2792984	0.95[EUR][1000 genomes]
rs2872538	0.96[EUR][1000 genomes]
rs2989563	0.85[EUR][1000 genomes]
rs3121188	0.84[EUR][1000 genomes]
rs3121190	0.85[EUR][1000 genomes]
rs3121191	0.90[EUR][1000 genomes]
rs3121192	0.92[EUR][1000 genomes]
rs3795777	0.96[EUR][1000 genomes]
rs3795782	0.83[EUR][1000 genomes]
rs4653536	0.81[EUR][1000 genomes]
rs4653543	0.95[EUR][1000 genomes]
rs4653545	0.92[EUR][1000 genomes]
rs4653931	0.97[EUR][1000 genomes]
rs4653933	0.94[EUR][1000 genomes]
rs4653934	0.84[EUR][1000 genomes]
rs489926	0.89[EUR][1000 genomes]
rs491293	0.91[EUR][1000 genomes]
rs493945	0.80[EUR][1000 genomes]
rs512406	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs545313	0.92[EUR][1000 genomes]
rs546967	0.92[EUR][1000 genomes]
rs55658545	0.84[EUR][1000 genomes]
rs55971985	0.94[EUR][1000 genomes]
rs56112646	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56168609	0.81[EUR][1000 genomes]
rs566640	0.92[EUR][1000 genomes]
rs61825279	0.81[EUR][1000 genomes]
rs61827540	0.97[EUR][1000 genomes]
rs6661539	0.84[EUR][1000 genomes]
rs72757829	0.82[EUR][1000 genomes]
rs7525075	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7532141	0.83[EUR][1000 genomes]
rs7532924	0.86[EUR][1000 genomes]
rs947087	0.97[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
rs1771470	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs1771470	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228402200-228425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:228402600-228418000	Strong transcription	Primary T cells from cord blood	blood
4	chr1:228403000-228428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:228403200-228418000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:228411800-228420200	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:228412400-228420400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:228412600-228420800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:228413000-228425600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:228413000-228426000	Weak transcription	Right Atrium	heart
11	chr1:228413000-228428400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:228413000-228428800	Weak transcription	Gastric	stomach
13	chr1:228413200-228418200	Weak transcription	Fetal Kidney	kidney
14	chr1:228413200-228420200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:228413200-228422400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:228413200-228424400	Weak transcription	Brain Anterior Caudate	brain
17	chr1:228413200-228426200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:228413400-228421000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:228413400-228426000	Weak transcription	Fetal Brain Male	brain
20	chr1:228413600-228418400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:228413600-228419200	Weak transcription	HSMMtube	muscle
22	chr1:228413600-228420400	Weak transcription	Primary B cells from cord blood	blood
23	chr1:228413600-228422200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:228413600-228428800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:228413800-228417800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:228413800-228428600	Weak transcription	Pancreas	Pancrea
27	chr1:228413800-228429000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:228414000-228419600	Weak transcription	A549	lung
29	chr1:228414000-228419800	Weak transcription	Fetal Heart	heart
30	chr1:228414200-228417800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:228414200-228418800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:228414400-228420200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:228414400-228420200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:228414400-228426000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:228414400-228426200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:228414400-228430400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:228415000-228421600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr1:228415200-228426000	Weak transcription	Spleen	Spleen
39	chr1:228415400-228420200	Weak transcription	Aorta	Aorta
40	chr1:228415400-228420200	Weak transcription	Lung	lung
41	chr1:228415800-228420200	Weak transcription	Fetal Intestine Small	intestine
42	chr1:228415800-228426000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:228416000-228418400	Weak transcription	Psoas Muscle	Psoas
44	chr1:228416000-228419400	Weak transcription	Right Ventricle	heart
45	chr1:228416000-228420000	Weak transcription	Fetal Intestine Large	intestine
46	chr1:228416000-228420200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:228416200-228418000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:228416200-228419400	Weak transcription	Left Ventricle	heart
49	chr1:228416200-228419800	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:228416200-228420000	Weak transcription	Fetal Stomach	stomach

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