Variant report

Variant	rs2298014
Chromosome Location	chr1:228362682-228362683
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228269154..228271874-chr1:228360119..228363775,3	K562	blood:
2	chr1:228362275..228366557-chr1:228367502..228371326,4	MCF-7	breast:
3	chr1:228362342..228364297-chr1:228644461..228646357,2	K562	blood:
4	chr1:228361423..228364297-chr1:228644461..228646940,2	K562	blood:
5	chr1:228360767..228363057-chr1:228399837..228402220,2	MCF-7	breast:
6	chr1:228350414..228357594-chr1:228359448..228365919,31	MCF-7	breast:
7	chr1:228296474..228298184-chr1:228362327..228363984,2	K562	blood:
8	chr1:228295318..228298683-chr1:228360322..228363984,4	K562	blood:
9	chr1:228296791..228299072-chr1:228362296..228364108,2	MCF-7	breast:
10	chr1:228331165..228333412-chr1:228361433..228363518,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000181218	Chromatin interaction
ENSG00000162913	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000143761	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1059778	0.83[EUR][1000 genomes]
rs10753445	0.81[EUR][1000 genomes]
rs10799468	0.82[EUR][1000 genomes]
rs10916268	0.82[EUR][1000 genomes]
rs10916271	0.83[EUR][1000 genomes]
rs10916277	0.90[EUR][1000 genomes]
rs12084338	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12097591	0.91[EUR][1000 genomes]
rs12130630	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12134624	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1411911	0.82[EUR][1000 genomes]
rs1557026	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1636195	0.82[ASN][1000 genomes]
rs17623766	0.91[EUR][1000 genomes]
rs17640616	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2185544	0.80[EUR][1000 genomes]
rs2313600	0.91[EUR][1000 genomes]
rs2313602	0.81[EUR][1000 genomes]
rs4653536	0.84[EUR][1000 genomes]
rs4653907	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653915	0.83[EUR][1000 genomes]
rs4653917	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653919	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653920	0.95[EUR][1000 genomes]
rs4653921	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55658545	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs55873533	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6426492	0.87[EUR][1000 genomes]
rs6657968	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6661539	0.81[EUR][1000 genomes]
rs6673893	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6682260	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72757811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72757812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72757824	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72757827	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72757829	0.86[EUR][1000 genomes]
rs7532141	0.81[EUR][1000 genomes]
rs7539762	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	esv3439695	chr1:228360954-228363502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
19	esv3439260	chr1:228361129-228363177	Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
20	esv3404829	chr1:228361629-228362727	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2298014	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354400-228384600	Weak transcription	Aorta	Aorta
2	chr1:228354600-228363600	Weak transcription	Primary B cells from cord blood	blood
3	chr1:228354600-228370400	Weak transcription	Right Atrium	heart
4	chr1:228354600-228382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
6	chr1:228354800-228362800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:228354800-228362800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:228354800-228362800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:228354800-228362800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:228354800-228363400	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:228354800-228364400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:228354800-228364400	Weak transcription	Brain Substantia Nigra	brain
13	chr1:228354800-228364600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:228354800-228365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:228354800-228366400	Weak transcription	Liver	Liver
16	chr1:228354800-228367000	Weak transcription	Osteobl	bone
17	chr1:228354800-228370800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:228354800-228371200	Weak transcription	HSMMtube	muscle
19	chr1:228354800-228373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:228355000-228362800	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:228355000-228364600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:228355000-228364800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:228355000-228364800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:228355000-228370600	Weak transcription	HepG2	liver
25	chr1:228355000-228372400	Weak transcription	Stomach Mucosa	stomach
26	chr1:228355000-228373200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:228355000-228373200	Weak transcription	Hela-S3	cervix
28	chr1:228355800-228364200	Strong transcription	Fetal Intestine Small	intestine
29	chr1:228358800-228362800	Weak transcription	Primary T cells from cord blood	blood
30	chr1:228359800-228363000	Enhancers	Placenta	Placenta
31	chr1:228361200-228366400	Genic enhancers	Fetal Stomach	stomach
32	chr1:228361400-228362800	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:228361400-228363200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr1:228361400-228363400	ZNF genes & repeats	Esophagus	oesophagus
35	chr1:228361600-228362800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
36	chr1:228361600-228362800	ZNF genes & repeats	Fetal Intestine Large	intestine
37	chr1:228361600-228362800	ZNF genes & repeats	Thymus	Thymus
38	chr1:228361800-228362800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:228361800-228363200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:228361800-228364000	Strong transcription	Colonic Mucosa	Colon
41	chr1:228361800-228364600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:228361800-228365800	Genic enhancers	Spleen	Spleen
43	chr1:228362200-228362800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:228362200-228362800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:228362200-228362800	Flanking Active TSS	K562	blood
46	chr1:228362200-228363000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:228362200-228363000	ZNF genes & repeats	Fetal Thymus	thymus
48	chr1:228362200-228363200	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:228362200-228364800	Strong transcription	Brain Germinal Matrix	brain
50	chr1:228362200-228365000	Strong transcription	Pancreas	Pancrea

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