Variant report

Variant	rs4653915
Chromosome Location	chr1:228364605-228364606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228362275..228366557-chr1:228367502..228371326,4	MCF-7	breast:
2	chr1:228301175..228302855-chr1:228364193..228366742,2	K562	blood:
3	chr1:228362968..228364679-chr1:228382995..228385252,2	K562	blood:
4	chr1:228350414..228357594-chr1:228359448..228365919,31	MCF-7	breast:
5	chr1:228359558..228361063-chr1:228363819..228365618,2	MCF-7	breast:
6	chr1:228362964..228365740-chr1:228389422..228392205,2	K562	blood:
7	chr1:228352925..228354845-chr1:228364134..228367346,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203684	Chromatin interaction
ENSG00000181873	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1059778	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10753445	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs10799468	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10799469	0.84[EUR][1000 genomes]
rs10799471	0.82[EUR][1000 genomes]
rs10916265	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs10916268	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10916271	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11584385	0.88[CEU][hapmap]
rs11799681	0.81[EUR][1000 genomes]
rs11804508	0.83[EUR][1000 genomes]
rs12024649	0.82[EUR][1000 genomes]
rs12084338	0.80[EUR][1000 genomes]
rs12130630	0.83[EUR][1000 genomes]
rs12134624	0.80[EUR][1000 genomes]
rs12564763	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs12726781	0.83[EUR][1000 genomes]
rs12745416	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1411910	0.88[CEU][hapmap]
rs1620111	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1629294	0.88[CEU][hapmap]
rs1757132	0.88[CEU][hapmap]
rs1757133	0.88[CEU][hapmap]
rs1757139	0.88[CEU][hapmap]
rs1757145	0.80[EUR][1000 genomes]
rs1757147	0.92[CEU][hapmap]
rs1757149	0.88[CEU][hapmap];0.80[CHB][hapmap]
rs1757150	0.88[CEU][hapmap]
rs1757152	0.88[CEU][hapmap]
rs1757156	0.88[CEU][hapmap]
rs1757158	0.80[EUR][1000 genomes]
rs1771459	0.88[CEU][hapmap]
rs1771460	0.88[CEU][hapmap]
rs1771461	0.87[CEU][hapmap]
rs1771462	0.87[CEU][hapmap]
rs1771467	0.87[CEU][hapmap]
rs1771472	0.87[CEU][hapmap]
rs1771474	0.88[CEU][hapmap]
rs1771476	0.88[CEU][hapmap]
rs1771479	0.88[CEU][hapmap]
rs1771482	0.88[CEU][hapmap]
rs1771483	0.88[CEU][hapmap]
rs1771484	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs1771485	0.88[CEU][hapmap]
rs1771487	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2066237	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs2185544	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2298014	0.83[EUR][1000 genomes]
rs2313601	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2313602	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2776853	0.83[EUR][1000 genomes]
rs2776855	0.88[CEU][hapmap]
rs2776856	0.88[CEU][hapmap]
rs2792984	0.80[EUR][1000 genomes]
rs2872538	0.88[CEU][hapmap]
rs3121191	0.81[EUR][1000 genomes]
rs3121192	0.82[EUR][1000 genomes]
rs4653536	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653907	0.80[EUR][1000 genomes]
rs4653917	0.81[EUR][1000 genomes]
rs4653919	0.81[EUR][1000 genomes]
rs4653920	0.80[EUR][1000 genomes]
rs4653921	0.81[EUR][1000 genomes]
rs493945	0.83[CEU][hapmap]
rs55873533	0.80[EUR][1000 genomes]
rs55971985	0.83[EUR][1000 genomes]
rs6673893	0.81[EUR][1000 genomes]
rs6682260	0.83[EUR][1000 genomes]
rs72757811	0.83[EUR][1000 genomes]
rs72757812	0.81[EUR][1000 genomes]
rs7512209	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs7532924	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7537636	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs7539762	0.81[EUR][1000 genomes]
rs947087	0.88[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
12	nsv873262	chr1:228340653-228371098	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
13	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
14	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
15	esv1806558	chr1:228358977-228365154	Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653915	OBSCN	cis	Esophagus Mucosa	GTEx
rs4653915	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354400-228384600	Weak transcription	Aorta	Aorta
2	chr1:228354600-228370400	Weak transcription	Right Atrium	heart
3	chr1:228354600-228382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
5	chr1:228354800-228365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:228354800-228366400	Weak transcription	Liver	Liver
7	chr1:228354800-228367000	Weak transcription	Osteobl	bone
8	chr1:228354800-228370800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:228354800-228371200	Weak transcription	HSMMtube	muscle
10	chr1:228354800-228373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:228355000-228364800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:228355000-228364800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:228355000-228370600	Weak transcription	HepG2	liver
14	chr1:228355000-228372400	Weak transcription	Stomach Mucosa	stomach
15	chr1:228355000-228373200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:228355000-228373200	Weak transcription	Hela-S3	cervix
17	chr1:228361200-228366400	Genic enhancers	Fetal Stomach	stomach
18	chr1:228361800-228365800	Genic enhancers	Spleen	Spleen
19	chr1:228362200-228364800	Strong transcription	Brain Germinal Matrix	brain
20	chr1:228362200-228365000	Strong transcription	Pancreas	Pancrea
21	chr1:228362400-228364800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:228362400-228364800	Strong transcription	Ovary	ovary
23	chr1:228362400-228365000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:228362400-228365000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:228362400-228365000	Strong transcription	Gastric	stomach
26	chr1:228362600-228364800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:228362600-228365000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:228362600-228365200	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:228362600-228365200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:228362600-228365400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:228362600-228365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:228362600-228365800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:228362600-228365800	Strong transcription	Fetal Brain Female	brain
34	chr1:228362600-228368600	Weak transcription	Psoas Muscle	Psoas
35	chr1:228362800-228364800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:228362800-228364800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:228362800-228364800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:228362800-228365000	Strong transcription	Fetal Intestine Large	intestine
39	chr1:228362800-228365200	Strong transcription	Thymus	Thymus
40	chr1:228362800-228365600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:228362800-228365600	Weak transcription	K562	blood
42	chr1:228362800-228366600	Strong transcription	Primary T cells from cord blood	blood
43	chr1:228363200-228364800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:228363200-228364800	Strong transcription	Placenta	Placenta
45	chr1:228363200-228364800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:228363200-228365200	Genic enhancers	Lung	lung
47	chr1:228363200-228366400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:228363200-228367200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:228363200-228368200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:228363200-228373200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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