Variant report

Variant	rs2276840
Chromosome Location	chr3:53891097-53891098
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53888852..53890407-chr3:53890829..53893730,2	K562	blood:
2	chr3:53889507..53891726-chr3:53914863..53916611,2	MCF-7	breast:
3	chr3:53882366..53883990-chr3:53889340..53891284,2	MCF-7	breast:
4	chr3:53878629..53881188-chr3:53889615..53893181,4	MCF-7	breast:
5	chr3:53889294..53893230-chr3:53913823..53917660,4	K562	blood:

Variant related genes	Relation type
ENSG00000113812	Chromatin interaction
ENSG00000016391	Chromatin interaction
ENSG00000056736	Chromatin interaction
ENSG00000222888	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1020082	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1134091	0.83[EUR][1000 genomes]
rs12632292	0.87[EUR][1000 genomes]
rs17053568	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17053590	0.84[CEU][hapmap]
rs1982171	0.84[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241806	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs2276843	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276844	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276845	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289203	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2304575	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304576	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs2884631	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3017	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733075	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3733079	0.84[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3733083	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821868	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821869	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41292476	0.83[EUR][1000 genomes]
rs4141606	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45511795	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687594	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs4687753	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687756	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4687758	0.84[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56743403	0.81[EUR][1000 genomes]
rs57398949	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62253003	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62253004	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6445612	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs709324	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7636856	0.85[CEU][hapmap]
rs9840445	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9849951	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9850063	0.87[EUR][1000 genomes]
rs9860367	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9880056	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs999514	0.85[CEU][hapmap]
rs999515	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2276840	IL17RB	cis	Cerebellum	GTEx
rs2276840	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs2276840	ACTR8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53881000-53892600	Weak transcription	Psoas Muscle	Psoas
2	chr3:53881000-53893200	Weak transcription	Ovary	ovary
3	chr3:53881200-53892400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:53881200-53895000	Weak transcription	A549	lung
5	chr3:53881200-53895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:53881400-53891400	Weak transcription	Brain Anterior Caudate	brain
7	chr3:53881400-53892000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:53881400-53892000	Weak transcription	Gastric	stomach
9	chr3:53881400-53892200	Weak transcription	Fetal Intestine Large	intestine
10	chr3:53881400-53892200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:53881400-53892600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:53881400-53892600	Weak transcription	Hela-S3	cervix
13	chr3:53881400-53892800	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:53881400-53893000	Weak transcription	Brain Angular Gyrus	brain
15	chr3:53881400-53893000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:53882400-53891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:53882600-53892200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:53882800-53892200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:53884000-53895800	Strong transcription	HepG2	liver
20	chr3:53884400-53892200	Weak transcription	Fetal Brain Female	brain
21	chr3:53884400-53892800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
23	chr3:53885200-53892200	Weak transcription	Fetal Lung	lung
24	chr3:53885400-53891200	Weak transcription	Fetal Stomach	stomach
25	chr3:53885400-53892400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:53885400-53892800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:53885400-53895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:53885600-53892200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:53885600-53892600	Weak transcription	Left Ventricle	heart
30	chr3:53885600-53896600	Weak transcription	Right Ventricle	heart
31	chr3:53886200-53897200	Weak transcription	Colonic Mucosa	Colon
32	chr3:53887600-53891200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:53887600-53892400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:53887800-53891200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:53887800-53892800	Weak transcription	Lung	lung
36	chr3:53887800-53898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:53888000-53892400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
39	chr3:53888800-53891800	Weak transcription	Brain Germinal Matrix	brain
40	chr3:53888800-53892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:53888800-53892600	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:53888800-53894400	Weak transcription	Primary T cells from cord blood	blood
43	chr3:53889000-53901400	Weak transcription	Esophagus	oesophagus
44	chr3:53889200-53892800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:53889200-53894400	Strong transcription	Fetal Intestine Small	intestine
46	chr3:53889400-53892800	Enhancers	GM12878-XiMat	blood
47	chr3:53889600-53892000	Strong transcription	Liver	Liver
48	chr3:53889600-53892200	Weak transcription	Adipose Nuclei	Adipose
49	chr3:53889600-53892600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:53889600-53892800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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