Variant report

Variant	rs4653889
Chromosome Location	chr1:228112121-228112122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228110564..228113344-chr1:228642639..228644578,2	K562	blood:
2	chr1:227935783..227938114-chr1:228110328..228112224,2	K562	blood:
3	chr1:228111067..228112932-chr1:228117820..228119468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10916245	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636192	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1774755	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2313118	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527614	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2527615	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2527616	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2796056	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3094912	0.84[CEU][hapmap]
rs3094915	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs590657	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591582	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs592736	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs594916	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs596208	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs596675	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs605410	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs621631	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs621963	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs632832	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs634106	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs635563	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs644794	0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs658238	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs672907	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs672977	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs673726	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs686533	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs849903	0.90[EUR][1000 genomes]
rs849904	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS 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	73 gene(s)	inside rSNPs	diseases
2	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
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	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
5	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
8	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	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
10	nsv873250	chr1:228051234-228121548	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
12	nsv826920	chr1:228106910-228116488	Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4653889	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228098600-228117600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:228098800-228122800	Weak transcription	HSMMtube	muscle
3	chr1:228099400-228122400	Weak transcription	HSMM	muscle
4	chr1:228103800-228113800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:228103800-228117000	Weak transcription	Fetal Intestine Large	intestine
6	chr1:228105200-228112400	Weak transcription	Brain Germinal Matrix	brain
7	chr1:228105200-228112800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:228106600-228121400	Weak transcription	Psoas Muscle	Psoas
9	chr1:228107600-228112200	Weak transcription	Fetal Heart	heart
10	chr1:228107800-228134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:228108200-228113000	Weak transcription	Colonic Mucosa	Colon
12	chr1:228108200-228113600	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr1:228108400-228112400	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:228109000-228113400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:228109200-228112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:228109200-228113600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:228109200-228117800	Weak transcription	Pancreas	Pancrea
18	chr1:228109400-228112200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:228109400-228112400	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:228109600-228112200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:228109600-228112800	Weak transcription	HMEC	breast
22	chr1:228109600-228132000	Weak transcription	Gastric	stomach
23	chr1:228109800-228112200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:228109800-228112600	Weak transcription	Esophagus	oesophagus
25	chr1:228109800-228112800	Weak transcription	Right Ventricle	heart
26	chr1:228109800-228117800	Weak transcription	Lung	lung
27	chr1:228109800-228134000	Weak transcription	Right Atrium	heart
28	chr1:228110000-228114000	Genic enhancers	Fetal Stomach	stomach
29	chr1:228110200-228112200	Genic enhancers	Fetal Muscle Leg	muscle
30	chr1:228110400-228113000	Enhancers	Fetal Lung	lung
31	chr1:228111000-228129800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:228111200-228113000	Strong transcription	Ovary	ovary
33	chr1:228111200-228116400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:228111200-228117000	Enhancers	Fetal Muscle Trunk	muscle
35	chr1:228111600-228114200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:228112000-228112200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:228112000-228112400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:228112000-228113000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:228112000-228113400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:228112000-228115200	Enhancers	Spleen	Spleen
41	chr1:228112000-228115400	Genic enhancers	Stomach Smooth Muscle	stomach

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