Variant report

Variant	rs6806287
Chromosome Location	chr3:20085199-20085200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20082249..20087148-chr3:20090873..20095169,4	K562	blood:
2	chr3:20081096..20083250-chr3:20083860..20086560,3	MCF-7	breast:
3	chr3:20083177..20086049-chr3:20086105..20087867,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114166	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10510496	0.89[CEU][hapmap]
rs11715597	0.89[CEU][hapmap]
rs17181086	0.89[CEU][hapmap]
rs17796169	0.89[CEU][hapmap]
rs17796242	0.89[CEU][hapmap]
rs1915919	0.88[ASW][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes]
rs1915922	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792745	0.89[CEU][hapmap]
rs6802632	0.89[CEU][hapmap]
rs6805894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7652967	0.86[AMR][1000 genomes]
rs9813441	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819915	0.82[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9822455	0.89[CEU][hapmap]
rs9840832	0.92[ASN][1000 genomes]
rs9849842	0.92[ASN][1000 genomes]
rs9852074	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858983	0.89[CEU][hapmap]
rs9882323	0.89[CEU][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6806287	RAB5A	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20082800-20085800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr3:20083000-20098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:20083200-20086200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr3:20083200-20088600	Weak transcription	Ovary	ovary
5	chr3:20083400-20085400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:20083400-20085400	Enhancers	Pancreas	Pancrea
7	chr3:20083400-20085600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:20083400-20085600	Flanking Active TSS	Thymus	Thymus
9	chr3:20083400-20085800	Enhancers	Fetal Intestine Large	intestine
10	chr3:20083400-20086200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:20083400-20086600	Enhancers	Placenta	Placenta
12	chr3:20083400-20089000	Weak transcription	Fetal Brain Male	brain
13	chr3:20083600-20085200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:20083600-20085400	Enhancers	Fetal Lung	lung
15	chr3:20083600-20085800	Enhancers	Primary hematopoietic stem cells	blood
16	chr3:20083800-20085400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr3:20083800-20085600	Enhancers	Fetal Muscle Leg	muscle
18	chr3:20083800-20086200	Enhancers	Fetal Heart	heart
19	chr3:20083800-20086200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr3:20083800-20086200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:20083800-20089200	Enhancers	Left Ventricle	heart
22	chr3:20083800-20092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:20084000-20085800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:20084000-20086200	Enhancers	Primary B cells from cord blood	blood
25	chr3:20084000-20089400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:20084000-20089400	Weak transcription	Brain Germinal Matrix	brain
27	chr3:20084000-20091200	Enhancers	Brain Substantia Nigra	brain
28	chr3:20084200-20085200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:20084200-20085600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:20084200-20085800	Enhancers	Stomach Mucosa	stomach
31	chr3:20084200-20085800	Flanking Active TSS	GM12878-XiMat	blood
32	chr3:20084200-20089400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:20084400-20085200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:20084400-20085200	Enhancers	Fetal Kidney	kidney
35	chr3:20084400-20085200	Genic enhancers	Fetal Stomach	stomach
36	chr3:20084400-20085200	Enhancers	Lung	lung
37	chr3:20084400-20085400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:20084400-20085800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr3:20084600-20085200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:20084600-20085200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr3:20084600-20085200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:20084600-20085200	Genic enhancers	Fetal Intestine Small	intestine
43	chr3:20084600-20085200	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr3:20084600-20085400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:20084600-20085400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:20084600-20085400	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr3:20084600-20085400	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr3:20084600-20085400	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr3:20084600-20085400	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr3:20084600-20085400	Flanking Active TSS	Dnd41	blood

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