Variant report

Variant	rs2170677
Chromosome Location	chr8:61537610-61537611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:61536011..61537750-chr8:61564924..61566806,2	K562	blood:
2	chr8:61527789..61530559-chr8:61535884..61538190,2	K562	blood:
3	chr8:61536123..61537975-chr8:61580798..61583756,2	K562	blood:
4	chr8:61534044..61535710-chr8:61537564..61539138,2	K562	blood:
5	chr8:61534210..61537266-chr8:61537564..61540249,3	K562	blood:
6	chr8:61525175..61527465-chr8:61536083..61538610,2	K562	blood:
7	chr8:61537605..61539859-chr8:61545071..61546845,2	K562	blood:

Variant related genes	Relation type
ENSG00000228862	Chromatin interaction
ENSG00000254869	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10100740	0.88[YRI][hapmap]
rs10957139	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10957141	0.88[YRI][hapmap]
rs11774286	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11778115	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11778529	0.88[YRI][hapmap]
rs11778888	0.88[YRI][hapmap]
rs11786146	0.88[YRI][hapmap]
rs11787141	0.89[EUR][1000 genomes]
rs13278228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2875966	0.88[YRI][hapmap]
rs603239	0.88[YRI][hapmap]
rs610455	0.88[YRI][hapmap]
rs649634	0.82[YRI][hapmap]
rs685715	0.90[EUR][1000 genomes]
rs6987523	0.88[YRI][hapmap]
rs6991529	0.88[YRI][hapmap]
rs6996344	0.82[YRI][hapmap]
rs7820349	0.88[YRI][hapmap]
rs7821738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7842105	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2170677	RAB2	cis	multi-tissue	Pritchard
rs2170677	RAB2	cis	uninvolved skin	skin_eQTL
rs2170677	RAB2	cis	lesional skin	skin_eQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61500400-61542200	Weak transcription	Hela-S3	cervix
2	chr8:61517800-61537800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr8:61519800-61541800	Weak transcription	Esophagus	oesophagus
4	chr8:61520200-61540000	Weak transcription	Fetal Intestine Small	intestine
5	chr8:61522000-61538000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr8:61522000-61538400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr8:61522000-61538800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:61522600-61538600	Weak transcription	Left Ventricle	heart
9	chr8:61522800-61538600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr8:61524200-61538600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr8:61529200-61538200	Strong transcription	Primary B cells from cord blood	blood
12	chr8:61532600-61538000	Weak transcription	Fetal Kidney	kidney
13	chr8:61532600-61539200	Weak transcription	Fetal Muscle Leg	muscle
14	chr8:61532600-61541600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr8:61532800-61538200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr8:61532800-61538200	Weak transcription	Brain Anterior Caudate	brain
17	chr8:61533400-61538200	Weak transcription	Primary T cells from cord blood	blood
18	chr8:61533400-61538200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr8:61533400-61538400	Weak transcription	Fetal Stomach	stomach
20	chr8:61533400-61538600	Weak transcription	Brain Hippocampus Middle	brain
21	chr8:61533600-61538400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr8:61534000-61539600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr8:61534200-61537800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr8:61534200-61537800	Weak transcription	NH-A	brain
25	chr8:61534200-61538000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr8:61534200-61538200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr8:61534200-61538400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr8:61534200-61540600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr8:61535000-61538000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr8:61535000-61538200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr8:61535000-61539200	Weak transcription	NHLF	lung
32	chr8:61535000-61542000	Weak transcription	A549	lung
33	chr8:61535200-61538000	Weak transcription	Osteobl	bone
34	chr8:61535200-61538600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr8:61535200-61538600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr8:61535400-61537800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr8:61535400-61537800	Weak transcription	Dnd41	blood
38	chr8:61535400-61538600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr8:61535400-61538600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr8:61535400-61541600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr8:61535400-61542200	Weak transcription	HSMMtube	muscle
42	chr8:61535600-61538600	Weak transcription	Adipose Nuclei	Adipose
43	chr8:61535600-61538800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr8:61535600-61538800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr8:61535600-61538800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr8:61535600-61539200	Weak transcription	Fetal Intestine Large	intestine
47	chr8:61535600-61541600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr8:61535800-61538000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr8:61535800-61538000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr8:61536000-61538400	Weak transcription	Placenta	Placenta

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