Variant report

Variant	rs612558
Chromosome Location	chr8:61566163-61566164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2054670	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2625442	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2680296	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2680297	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2680298	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs597123	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs601778	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs608740	0.82[CEU][hapmap];0.95[JPT][hapmap]
rs609264	0.90[JPT][hapmap]
rs617434	0.86[JPT][hapmap]
rs618190	0.85[JPT][hapmap]
rs622755	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs623845	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs623917	0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs625979	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs626913	0.90[JPT][hapmap]
rs629523	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs645067	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs645765	0.82[ASN][1000 genomes]
rs657718	0.96[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]
rs658176	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs659805	0.92[ASN][1000 genomes]
rs665893	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs671204	0.80[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes]
rs671576	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs673802	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs685985	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs686852	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs687351	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7822621	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530383	chr8:61431756-61605551	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv831335	chr8:61497540-61688992	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv890945	chr8:61522008-61707725	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS 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	33 gene(s)	inside rSNPs	diseases
5	nsv824657	chr8:61555227-61626758	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv824658	chr8:61561488-61612108	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs612558	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61563400-61566400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr8:61563400-61566400	Active TSS	Right Atrium	heart
3	chr8:61563400-61566400	Active TSS	HSMMtube	muscle
4	chr8:61563400-61566800	Active TSS	Sigmoid Colon	Sigmoid Colon
5	chr8:61563400-61567200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr8:61563600-61566200	Active TSS	A549	lung
7	chr8:61563600-61566800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr8:61563600-61566800	Active TSS	Placenta Amnion	Placenta Amnion
9	chr8:61563600-61566800	Active TSS	Psoas Muscle	Psoas
10	chr8:61563600-61566800	Active TSS	Right Ventricle	heart
11	chr8:61563800-61566600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:61563800-61566800	Active TSS	Brain Anterior Caudate	brain
13	chr8:61563800-61566800	Active TSS	Brain Hippocampus Middle	brain
14	chr8:61563800-61566800	Active TSS	Brain Substantia Nigra	brain
15	chr8:61563800-61566800	Active TSS	Fetal Intestine Large	intestine
16	chr8:61563800-61566800	Active TSS	GM12878-XiMat	blood
17	chr8:61564000-61566400	Active TSS	Esophagus	oesophagus
18	chr8:61564000-61566400	Active TSS	Spleen	Spleen
19	chr8:61564000-61566600	Active TSS	Ovary	ovary
20	chr8:61564000-61566800	Active TSS	Gastric	stomach
21	chr8:61564200-61566200	Flanking Bivalent TSS/Enh	Thymus	Thymus
22	chr8:61564200-61566400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
23	chr8:61564200-61566600	Active TSS	Primary B cells from peripheral blood	blood
24	chr8:61564200-61566800	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr8:61564200-61566800	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr8:61564400-61566600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr8:61564400-61566800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr8:61565000-61566200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr8:61565000-61566800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr8:61565000-61566800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr8:61565200-61566200	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr8:61565200-61566200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr8:61565200-61566200	Flanking Active TSS	Liver	Liver
34	chr8:61565200-61566200	Flanking Active TSS	HMEC	breast
35	chr8:61565200-61566800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr8:61565200-61566800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
37	chr8:61565200-61567000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr8:61565200-61567000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
39	chr8:61565200-61567000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr8:61565400-61566200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr8:61565400-61566200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr8:61565400-61566400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
43	chr8:61565400-61566400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr8:61565400-61566400	Flanking Bivalent TSS/Enh	Osteobl	bone
45	chr8:61565400-61566600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr8:61565400-61566600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr8:61565400-61566600	Flanking Active TSS	K562	blood
48	chr8:61565400-61566800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
49	chr8:61565400-61566800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
50	chr8:61565400-61566800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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