Variant report

Variant	rs2948087
Chromosome Location	chr3:20099215-20099216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20081053..20084896-chr3:20098793..20102867,5	K562	blood:
2	chr3:19988087..19989789-chr3:20097450..20099534,2	MCF-7	breast:
3	chr3:20079576..20083677-chr3:20098793..20102064,4	K562	blood:

Variant related genes	Relation type
ENSG00000114166	Chromatin interaction
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11128936	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs12636488	0.81[ASN][1000 genomes]
rs2293139	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2623075	0.88[EUR][1000 genomes]
rs2661376	0.80[CEU][hapmap]
rs2661377	1.00[CEU][hapmap]
rs2686315	0.80[CEU][hapmap]
rs2929399	1.00[EUR][1000 genomes]
rs2929400	0.98[EUR][1000 genomes]
rs2929403	0.90[CEU][hapmap];0.98[EUR][1000 genomes]
rs2929405	0.98[EUR][1000 genomes]
rs2948083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2948086	0.84[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2948088	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3804574	0.91[CEU][hapmap]
rs60355368	0.86[EUR][1000 genomes]
rs6784715	0.82[EUR][1000 genomes]
rs939851	0.85[EUR][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	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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2948087	RAB5A	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20086200-20102800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:20087600-20099400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr3:20090800-20100600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:20094200-20099400	Enhancers	Fetal Thymus	thymus
5	chr3:20095400-20099600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr3:20095600-20099400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:20095600-20099600	Enhancers	Liver	Liver
8	chr3:20095600-20099800	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:20095600-20100000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:20095600-20100200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr3:20095600-20100200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:20095600-20100400	Enhancers	Fetal Heart	heart
13	chr3:20095600-20100800	Enhancers	Placenta	Placenta
14	chr3:20095800-20099400	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:20095800-20099400	Enhancers	Brain Angular Gyrus	brain
16	chr3:20095800-20099400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr3:20095800-20099600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:20095800-20099600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:20095800-20099600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:20095800-20099600	Enhancers	Adipose Nuclei	Adipose
21	chr3:20095800-20099600	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:20095800-20099600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr3:20095800-20099600	Enhancers	HMEC	breast
24	chr3:20095800-20099800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:20095800-20099800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:20095800-20099800	Enhancers	Fetal Muscle Leg	muscle
27	chr3:20095800-20099800	Enhancers	Spleen	Spleen
28	chr3:20095800-20099800	Enhancers	HUVEC	blood vessel
29	chr3:20095800-20100400	Enhancers	Fetal Lung	lung
30	chr3:20095800-20100400	Enhancers	Psoas Muscle	Psoas
31	chr3:20095800-20100600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:20096000-20099400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:20096000-20099600	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr3:20096000-20099600	Enhancers	K562	blood
35	chr3:20096000-20100200	Enhancers	Small Intestine	intestine
36	chr3:20096000-20100800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr3:20096200-20099600	Enhancers	Colon Smooth Muscle	Colon
38	chr3:20096400-20099400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:20096400-20099400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr3:20096600-20099400	Enhancers	A549	lung
41	chr3:20096600-20099600	Enhancers	Brain Substantia Nigra	brain
42	chr3:20096600-20106400	Weak transcription	Fetal Intestine Large	intestine
43	chr3:20096800-20099600	Enhancers	Hela-S3	cervix
44	chr3:20096800-20100600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:20096800-20102600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:20097000-20099400	Enhancers	GM12878-XiMat	blood
47	chr3:20097000-20099600	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr3:20097000-20100400	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr3:20097200-20099400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr3:20097200-20100200	Enhancers	Brain Hippocampus Middle	brain

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