Variant report

Variant	rs2289203
Chromosome Location	chr3:53906663-53906664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53901985..53904512-chr3:53906172..53908429,2	K562	blood:

Variant related genes	Relation type
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1020082	0.92[EUR][1000 genomes]
rs1134091	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12632292	0.93[EUR][1000 genomes]
rs17053568	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17053590	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1982171	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2241806	1.00[CEU][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs2276840	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2276843	0.92[EUR][1000 genomes]
rs2276844	0.92[EUR][1000 genomes]
rs2276845	0.92[EUR][1000 genomes]
rs2304575	0.89[EUR][1000 genomes]
rs2304576	1.00[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs2884631	0.82[EUR][1000 genomes]
rs3017	0.81[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs3733075	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs3733079	1.00[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs3733083	0.91[EUR][1000 genomes]
rs3821868	0.81[EUR][1000 genomes]
rs3821869	0.84[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs41292476	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4141606	0.90[EUR][1000 genomes]
rs45511795	0.93[EUR][1000 genomes]
rs4687594	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4687753	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs4687756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687758	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4687760	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55917919	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56743403	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57398949	0.91[EUR][1000 genomes]
rs6445612	1.00[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs709324	0.82[EUR][1000 genomes]
rs73078007	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9840445	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9849951	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9850063	0.93[EUR][1000 genomes]
rs9860367	0.82[EUR][1000 genomes]
rs9880056	1.00[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs999515	0.96[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2289203	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs2289203	ACTR8	cis	parietal	SCAN
rs2289203	IL17RB	cis	cerebellum	SCAN
rs2289203	SFMBT1	cis	cerebellum	SCAN
rs2289203	PHF7	cis	cerebellum	SCAN
rs2289203	ACTR8	cis	cerebellum	SCAN
rs2289203	IL17RB	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
2	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53891000-53914200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:53891000-53914200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr3:53891200-53910800	Strong transcription	Fetal Stomach	stomach
7	chr3:53891400-53914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:53891800-53912800	Strong transcription	Brain Germinal Matrix	brain
9	chr3:53892000-53914400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:53892200-53912400	Strong transcription	Fetal Brain Female	brain
11	chr3:53892200-53914000	Strong transcription	Adipose Nuclei	Adipose
12	chr3:53892200-53914400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:53892200-53914600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:53892400-53913000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:53892400-53913800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:53892400-53914200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr3:53892400-53914400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:53892600-53914200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:53892600-53914400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:53892600-53914400	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:53892800-53914200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:53892800-53914200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr3:53892800-53914200	Strong transcription	Thymus	Thymus
24	chr3:53892800-53914400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:53892800-53914600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr3:53893000-53914000	Strong transcription	Placenta	Placenta
27	chr3:53893000-53914400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:53893200-53914000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:53893200-53914200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:53893200-53914200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:53893200-53914200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:53893200-53914600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:53893400-53908200	Weak transcription	K562	blood
34	chr3:53893400-53914200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:53893800-53912800	Strong transcription	Brain Anterior Caudate	brain
36	chr3:53894200-53914400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:53894400-53914000	Strong transcription	Primary T cells from cord blood	blood
38	chr3:53894400-53914400	Strong transcription	Fetal Thymus	thymus
39	chr3:53894800-53914200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr3:53894800-53914200	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr3:53895000-53914000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:53895000-53914200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:53895000-53914400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:53895200-53908800	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr3:53895200-53913200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:53895200-53914200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:53895200-53914200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:53895200-53914200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:53895400-53913800	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:53895600-53914200	Strong transcription	Rectal Mucosa Donor 31	rectum

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