Variant report

Variant	rs12261690
Chromosome Location	chr10:27814553-27814554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:27814281..27821266-chr10:27824273..27827197,8	K562	blood:
2	chr10:27807125..27810398-chr10:27814464..27816469,3	K562	blood:
3	chr10:27814407..27819485-chr10:27827965..27831348,4	K562	blood:
4	chr10:27808762..27810610-chr10:27813283..27816177,3	K562	blood:
5	chr10:27802914..27806574-chr10:27810162..27816250,5	MCF-7	breast:
6	chr10:27791661..27794464-chr10:27811491..27814679,3	K562	blood:
7	chr10:27813292..27818525-chr10:27818980..27823484,5	K562	blood:

Variant related genes	Relation type
ENSG00000099246	Chromatin interaction

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];1.00[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];0.85[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];0.85[AMR][1000 genomes]
rs11015838	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015842	0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015844	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015848	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.85[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];0.85[AMR][1000 genomes]
rs11015851	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015852	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015853	0.88[AFR][1000 genomes]
rs11015859	1.00[MEX][hapmap];0.83[MKK][hapmap]
rs12242968	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12248740	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]
rs12249534	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12253290	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12254670	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12258435	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12260532	1.00[AFR][1000 genomes];0.85[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];0.85[AMR][1000 genomes]
rs12263216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12267298	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2368234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59498921	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60909738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61486615	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9651381	0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[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
rs12261690	RAB18	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27794200-27817000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:27794400-27824000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr10:27794400-27837400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:27794800-27814600	Weak transcription	HSMMtube	muscle
5	chr10:27794800-27822800	Weak transcription	Colonic Mucosa	Colon
6	chr10:27794800-27823200	Weak transcription	Esophagus	oesophagus
7	chr10:27794800-27823200	Weak transcription	Spleen	Spleen
8	chr10:27795200-27816800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr10:27795600-27814800	Weak transcription	Pancreas	Pancrea
10	chr10:27795600-27816800	Weak transcription	Brain Hippocampus Middle	brain
11	chr10:27795800-27822600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr10:27795800-27832600	Weak transcription	Small Intestine	intestine
13	chr10:27796000-27814600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr10:27800800-27823200	Weak transcription	Brain Anterior Caudate	brain
15	chr10:27801000-27815200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr10:27801000-27816600	Weak transcription	HUVEC	blood vessel
17	chr10:27801800-27829000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr10:27803200-27818200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr10:27803200-27822600	Weak transcription	NH-A	brain
20	chr10:27803400-27822400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr10:27803400-27823200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr10:27803400-27823800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:27803400-27830800	Weak transcription	Hela-S3	cervix
24	chr10:27803800-27814600	Weak transcription	Osteobl	bone
25	chr10:27803800-27817000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:27803800-27817200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr10:27804000-27814800	Weak transcription	HSMM	muscle
28	chr10:27804000-27816800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr10:27804000-27817400	Weak transcription	Fetal Muscle Leg	muscle
30	chr10:27804000-27817600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr10:27804000-27822600	Weak transcription	Dnd41	blood
32	chr10:27804000-27823000	Weak transcription	Lung	lung
33	chr10:27804000-27823000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr10:27804000-27823200	Weak transcription	Gastric	stomach
35	chr10:27804000-27823400	Weak transcription	Aorta	Aorta
36	chr10:27804200-27814600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:27804200-27814800	Weak transcription	Adipose Nuclei	Adipose
38	chr10:27804200-27818200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:27804200-27822400	Weak transcription	HMEC	breast
40	chr10:27804200-27822600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr10:27804400-27822800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr10:27804600-27814800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr10:27804600-27814800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr10:27804600-27816800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr10:27804600-27822600	Weak transcription	Placenta	Placenta
46	chr10:27804600-27823000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr10:27804600-27823000	Weak transcription	Fetal Intestine Large	intestine
48	chr10:27805200-27815200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:27805600-27814800	Weak transcription	Fetal Stomach	stomach
50	chr10:27805600-27822800	Weak transcription	Fetal Thymus	thymus

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