Variant report

Variant	rs12248740
Chromosome Location	chr10:27827367-27827368
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:27823448..27828239-chr10:27829759..27835759,6	K562	blood:
2	chr10:27803807..27806006-chr10:27825397..27828002,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB18-3	chr10:27826994-27827441	NONHSAT011909

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10437434	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10508723	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10764699	0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs11015830	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015838	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015842	0.87[YRI][hapmap];0.91[AFR][1000 genomes]
rs11015844	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015848	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015850	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015851	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015853	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015859	1.00[MEX][hapmap];0.83[MKK][hapmap]
rs12242968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12249534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12253290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12254670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12258435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261373	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261690	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12263216	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12267298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2368234	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59498921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60909738	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61486615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9651381	0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]

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	nsv8614	chr10:27504487-27828406	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv550241	chr10:27569521-28025771	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1045257	chr10:27572440-27926946	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1053952	chr10:27659365-27915029	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12248740	RAB18	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27794400-27837400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:27795800-27832600	Weak transcription	Small Intestine	intestine
3	chr10:27801800-27829000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr10:27803400-27830800	Weak transcription	Hela-S3	cervix
5	chr10:27814200-27836000	Weak transcription	Brain Germinal Matrix	brain
6	chr10:27815000-27831000	Weak transcription	Fetal Heart	heart
7	chr10:27815000-27834400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:27815600-27831600	Weak transcription	Psoas Muscle	Psoas
9	chr10:27818400-27828000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:27818800-27830800	Weak transcription	Stomach Mucosa	stomach
11	chr10:27820400-27829400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr10:27820400-27835200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr10:27820600-27829400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr10:27821400-27828600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:27821400-27829600	Strong transcription	HSMM	muscle
16	chr10:27821800-27828200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr10:27821800-27829600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:27821800-27830000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr10:27822000-27828400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr10:27822200-27830000	Strong transcription	Primary B cells from cord blood	blood
21	chr10:27822200-27835200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr10:27822400-27828400	Strong transcription	HMEC	breast
23	chr10:27822400-27829400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr10:27822400-27831600	Strong transcription	Osteobl	bone
25	chr10:27822400-27832000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr10:27822600-27827800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:27822600-27827800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr10:27822600-27827800	Strong transcription	HepG2	liver
29	chr10:27822600-27828000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr10:27822600-27828000	Strong transcription	Fetal Lung	lung
31	chr10:27822600-27828200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr10:27822600-27828600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr10:27822600-27829200	Strong transcription	Placenta	Placenta
34	chr10:27822600-27829400	Strong transcription	Liver	Liver
35	chr10:27822600-27830200	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr10:27822600-27832400	Strong transcription	Adipose Nuclei	Adipose
37	chr10:27822600-27832400	Strong transcription	Dnd41	blood
38	chr10:27822600-27832800	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr10:27822800-27827400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr10:27822800-27828000	Strong transcription	Primary T cells from cord blood	blood
41	chr10:27822800-27828000	Strong transcription	Fetal Thymus	thymus
42	chr10:27822800-27828000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr10:27822800-27828200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr10:27822800-27828200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr10:27822800-27828400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr10:27822800-27828800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr10:27823000-27827800	Strong transcription	Fetal Intestine Large	intestine
48	chr10:27823000-27828000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr10:27823000-27828000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr10:27823000-27828000	Strong transcription	Rectal Mucosa Donor 29	rectum

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