Variant report

Variant	rs2948091
Chromosome Location	chr3:20065662-20065663
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	chr3:20064524..20066130-chr3:20225214..20227213,2	K562	blood:
2	chr3:20001354..20003479-chr3:20064467..20066486,2	K562	blood:
3	chr3:20064379..20066103-chr3:20069480..20072008,2	MCF-7	breast:
4	chr3:20059399..20061509-chr3:20063864..20066520,2	K562	blood:
5	chr3:20035142..20037256-chr3:20064733..20066737,2	K562	blood:
6	chr3:20050259..20051981-chr3:20063056..20065911,2	K562	blood:
7	chr3:20063707..20066137-chr3:20066791..20068854,2	K562	blood:
8	chr3:20053905..20056718-chr3:20064582..20067158,2	K562	blood:
9	chr3:20061429..20065762-chr3:20080168..20083220,6	K562	blood:
10	chr3:20063995..20066056-chr3:20077383..20080079,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000129810	Chromatin interaction
ENSG00000229468	Chromatin interaction
ENSG00000114166	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2170342	0.83[TSI][hapmap]
rs2623078	0.86[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2686325	0.93[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2929386	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2929412	0.83[EUR][1000 genomes]
rs2948099	0.85[EUR][1000 genomes]
rs2948100	0.83[EUR][1000 genomes]
rs2948103	0.84[EUR][1000 genomes]
rs2948104	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2948107	0.83[EUR][1000 genomes]
rs6550273	0.84[EUR][1000 genomes]
rs6778866	0.90[TSI][hapmap]
rs9942096	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases
10	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2948091	RAB5A	cis	parietal	SCAN
rs2948091	EFHB,LOC100130288	cis	brain	BrainEAC
rs2948091	EFHB	cis	multi-tissue	Pritchard

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20056600-20080000	Weak transcription	Right Atrium	heart
2	chr3:20064000-20065800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:20064200-20065800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:20064200-20066000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:20064400-20065800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:20064400-20065800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:20064400-20065800	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr3:20064400-20065800	Enhancers	Brain Substantia Nigra	brain
9	chr3:20064400-20065800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr3:20064400-20066000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:20064400-20066000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:20064400-20066000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:20064600-20065800	Enhancers	Brain Cingulate Gyrus	brain
14	chr3:20064600-20065800	Enhancers	Brain Hippocampus Middle	brain
15	chr3:20064600-20065800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:20064600-20065800	Enhancers	Duodenum Mucosa	Duodenum
17	chr3:20064600-20065800	Enhancers	Rectal Smooth Muscle	rectum
18	chr3:20064600-20066000	Enhancers	Primary hematopoietic stem cells	blood
19	chr3:20064600-20066000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:20064600-20066000	Enhancers	Brain Angular Gyrus	brain
21	chr3:20064600-20066000	Enhancers	Fetal Intestine Large	intestine
22	chr3:20064600-20066000	Enhancers	Fetal Intestine Small	intestine
23	chr3:20064600-20066200	Enhancers	Adipose Nuclei	Adipose
24	chr3:20064600-20066600	Enhancers	Left Ventricle	heart
25	chr3:20064800-20065800	Enhancers	Brain Anterior Caudate	brain
26	chr3:20064800-20065800	Enhancers	Colon Smooth Muscle	Colon
27	chr3:20065000-20065800	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr3:20065000-20065800	Enhancers	Right Ventricle	heart
29	chr3:20065000-20065800	Enhancers	Stomach Mucosa	stomach
30	chr3:20065000-20066000	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr3:20065000-20066000	Enhancers	Primary B cells from peripheral blood	blood
32	chr3:20065200-20065800	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr3:20065200-20066000	Enhancers	Fetal Thymus	thymus
34	chr3:20065400-20065800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:20065400-20066000	Enhancers	Primary B cells from cord blood	blood
36	chr3:20065400-20066200	Enhancers	K562	blood
37	chr3:20065600-20065800	Enhancers	Stomach Smooth Muscle	stomach
38	chr3:20065600-20066000	Enhancers	HUVEC	blood vessel

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