Variant report

Variant	rs12261373
Chromosome Location	chr10:27792683-27792684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:27792614-27793956	H1-hESC	embryonic stem cell:	n/a	n/a
2	RELA	chr10:27792471-27793482	GM15510	blood:	n/a	n/a
3	POLR2A	chr10:27792627-27793625	GM12878	blood:	n/a	n/a
4	TBP	chr10:27792657-27793662	K562	blood:	n/a	n/a
5	TCF3	chr10:27792590-27793540	GM12878	blood:	n/a	n/a
6	RCOR1	chr10:27792614-27793491	K562	blood:	n/a	n/a
7	BRCA1	chr10:27792637-27793337	Hela-S3	cervix:	n/a	n/a
8	MTA3	chr10:27792583-27793639	GM12878	blood:	n/a	n/a
9	MAX	chr10:27792543-27793488	GM12878	blood:	n/a	n/a
10	POLR2A	chr10:27792649-27793496	HCT-116	colon:	n/a	n/a
11	ELF1	chr10:27792681-27793565	MCF-7	breast:	n/a	chr10:27793473-27793485
12	POLR2A	chr10:27792578-27793677	U87	brain:	n/a	n/a
13	MAZ	chr10:27792631-27793577	K562	blood:	n/a	n/a
14	CHD2	chr10:27792677-27793469	GM12878	blood:	n/a	n/a
15	ZNF143	chr10:27792641-27793426	H1-hESC	embryonic stem cell:	n/a	chr10:27793105-27793123
16	GATA2	chr10:27792611-27793092	K562	blood:	n/a	n/a
17	ZNF143	chr10:27792647-27793488	GM12878	blood:	n/a	chr10:27793445-27793454 chr10:27793105-27793123
18	MAX	chr10:27792652-27793651	HepG2	liver:	n/a	n/a
19	POLR2A	chr10:27792548-27793585	Raji	blood:	n/a	n/a
20	POLR2A	chr10:27792619-27793637	HUVEC	blood vessel:	n/a	n/a
21	USF2	chr10:27792524-27793379	GM12878	blood:	n/a	n/a
22	ELF1	chr10:27792664-27793594	HCT-116	colon:	n/a	chr10:27793473-27793485
23	EP300	chr10:27792634-27793399	GM12878	blood:	n/a	chr10:27793047-27793063
24	POLR2A	chr10:27792651-27793514	U87	brain:	n/a	n/a
25	JUND	chr10:27792665-27793486	K562	blood:	n/a	n/a
26	MAX	chr10:27792683-27793574	A549	lung:	n/a	n/a
27	MAX	chr10:27792643-27793662	A549	lung:	n/a	n/a
28	PML	chr10:27792635-27793482	K562	blood:	n/a	n/a
29	PML	chr10:27792593-27794067	GM12878	blood:	n/a	chr10:27793801-27793809
30	EP300	chr10:27792646-27793564	ECC-1	luminal epithelium:	n/a	chr10:27793047-27793063
31	MYC	chr10:27792506-27793792	K562	blood:	n/a	n/a
32	ZNF263	chr10:27792445-27793722	HEK293-T-REx	kidney:	n/a	chr10:27792981-27793002
33	NR2F2	chr10:27792682-27793413	K562	blood:	n/a	n/a
34	POLR2A	chr10:27792624-27793620	GM12892	blood:	n/a	n/a
35	MAFK	chr10:27792655-27793365	K562	blood:	n/a	chr10:27793186-27793201
36	IRF1	chr10:27792656-27793380	K562	blood:	n/a	n/a
37	POLR2A	chr10:27792494-27793905	HepG2	liver:	n/a	n/a
38	ZMIZ1	chr10:27792643-27793477	K562	blood:	n/a	n/a
39	POLR2A	chr10:27792623-27793789	MCF-7	breast:	n/a	n/a
40	ZNF384	chr10:27792626-27793246	GM12878	blood:	n/a	n/a
41	TBL1XR1	chr10:27792406-27793394	K562	blood:	n/a	n/a
42	NRF1	chr10:27792291-27793586	SK-N-SH	brain:	n/a	chr10:27793214-27793225 chr10:27793211-27793225 chr10:27793061-27793072 chr10:27793061-27793075 chr10:27793063-27793072 chr10:27793216-27793225 chr10:27793058-27793072 chr10:27793061-27793072 chr10:27793214-27793223
43	NR2F2	chr10:27792612-27793593	K562	blood:	n/a	n/a
44	CEBPD	chr10:27792636-27793509	K562	blood:	n/a	n/a
45	HCFC1	chr10:27792328-27793661	Hela-S3	cervix:	n/a	n/a
46	CEBPB	chr10:27792532-27793659	GM12878	blood:	n/a	n/a
47	TAL1	chr10:27792590-27793387	K562	blood:	n/a	n/a
48	TEAD4	chr10:27792593-27793354	K562	blood:	n/a	n/a
49	E2F6	chr10:27792549-27793631	K562	blood:	n/a	chr10:27793215-27793224 chr10:27793062-27793071
50	STAT5A	chr10:27792625-27793538	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:27790605..27793100-chr10:27816986..27820161,3	K562	blood:

Variant related genes	Relation type
RAB18	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10437434	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10508723	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10764699	0.87[YRI][hapmap];0.93[AFR][1000 genomes]
rs11015815	0.84[AFR][1000 genomes]
rs11015830	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015838	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015842	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs11015844	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015848	0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015850	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]
rs11015851	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015852	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015853	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015859	1.00[MEX][hapmap]
rs12242968	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12244699	0.84[AFR][1000 genomes]
rs12248740	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]
rs12249534	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12253290	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12254670	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12256731	0.83[AFR][1000 genomes]
rs12258435	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260532	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261690	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	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12267298	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1989581	0.84[AFR][1000 genomes]
rs2368234	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58800730	0.84[AFR][1000 genomes]
rs59498921	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60909738	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61226328	0.84[AFR][1000 genomes]
rs61486615	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9651381	0.87[YRI][hapmap];0.86[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
rs12261373	RAB18	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27790000-27792800	Weak transcription	Esophagus	oesophagus
2	chr10:27792400-27792800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:27792400-27792800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:27792400-27792800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr10:27792400-27792800	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:27792400-27792800	Enhancers	Primary hematopoietic stem cells	blood
7	chr10:27792400-27792800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr10:27792400-27792800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr10:27792400-27792800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr10:27792400-27792800	Flanking Active TSS	Fetal Lung	lung
11	chr10:27792400-27792800	Enhancers	Lung	lung
12	chr10:27792400-27792800	Enhancers	Pancreas	Pancrea
13	chr10:27792400-27792800	Enhancers	Psoas Muscle	Psoas
14	chr10:27792400-27792800	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr10:27792400-27792800	Flanking Active TSS	Thymus	Thymus
16	chr10:27792400-27792800	Flanking Active TSS	A549	lung
17	chr10:27792400-27792800	Flanking Active TSS	NHDF-Ad	bronchial
18	chr10:27792400-27793000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:27792400-27793000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr10:27792400-27793000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:27792400-27793000	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr10:27792400-27793000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr10:27792400-27793000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:27792400-27793000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr10:27792400-27793000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:27792400-27793000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr10:27792400-27793000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:27792400-27793000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:27792400-27793000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr10:27792400-27793000	Flanking Active TSS	Fetal Thymus	thymus
31	chr10:27792400-27793000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr10:27792400-27793000	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr10:27792400-27793000	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr10:27792400-27793000	Flanking Active TSS	Dnd41	blood
35	chr10:27792400-27793000	Flanking Active TSS	GM12878-XiMat	blood
36	chr10:27792400-27793000	Flanking Active TSS	Hela-S3	cervix
37	chr10:27792400-27793000	Flanking Active TSS	K562	blood
38	chr10:27792400-27793200	Active TSS	Brain Germinal Matrix	brain
39	chr10:27792400-27793800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:27792400-27794200	Active TSS	Fetal Brain Male	brain
41	chr10:27792400-27794400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr10:27792400-27794600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr10:27792400-27794800	Active TSS	Fetal Kidney	kidney
44	chr10:27792400-27795000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr10:27792600-27792800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr10:27792600-27792800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr10:27792600-27792800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr10:27792600-27792800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr10:27792600-27792800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:27792600-27792800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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