Variant report

Variant	rs12364701
Chromosome Location	chr11:120203652-120203653
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr11:120203260-120204047	GM12878	blood:	n/a	n/a
2	SPI1	chr11:120203551-120203837	GM12891	blood:	n/a	n/a
3	SPI1	chr11:120203520-120203919	HL-60	blood:	n/a	n/a
4	GATA3	chr11:120203560-120204431	SK-N-SH	brain:	n/a	n/a
5	SPI1	chr11:120203525-120203862	GM12891	blood:	n/a	n/a
6	NFIC	chr11:120203565-120204314	SK-N-SH	brain:	n/a	n/a
7	SPI1	chr11:120203588-120203833	K562	blood:	n/a	n/a
8	ZNF384	chr11:120203588-120203966	K562	blood:	n/a	n/a
9	ZNF384	chr11:120203597-120204280	GM12878	blood:	n/a	n/a
10	SPI1	chr11:120203550-120203905	HL-60	blood:	n/a	n/a
11	SPI1	chr11:120203517-120203907	GM12878	blood:	n/a	n/a
12	SPI1	chr11:120203555-120203835	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:120197781..120201028-chr11:120203553..120206762,3	MCF-7	breast:
2	chr11:120193025..120195977-chr11:120201525..120204056,3	K562	blood:
3	chr11:120106244..120107805-chr11:120202318..120204385,2	K562	blood:
4	chr11:120202465..120204611-chr11:120208153..120210823,2	K562	blood:
5	chr11:120201225..120203829-chr11:120204191..120207304,3	K562	blood:
6	chr11:120106365..120107959-chr11:120202588..120204989,2	MCF-7	breast:
7	chr11:120202870..120205056-chr11:120277472..120279353,2	K562	blood:
8	chr11:120194862..120197585-chr11:120203291..120207610,4	MCF-7	breast:

No data

Variant related genes	Relation type
ARHGEF12	TF binding region
ENSG00000181264	Chromatin interaction
ENSG00000137709	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10892559	1.00[CHB][hapmap]
rs11217817	1.00[CHB][hapmap]
rs1941409	1.00[ASN][1000 genomes]
rs1941411	1.00[CHB][hapmap]
rs2155808	1.00[CHB][hapmap]
rs2155809	1.00[CHB][hapmap]
rs2715881	1.00[CHB][hapmap]
rs2715883	1.00[CHB][hapmap]
rs2847494	1.00[CHB][hapmap]
rs2847495	1.00[CHB][hapmap]
rs622373	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7484249	1.00[CHB][hapmap]
rs7930543	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12364701	ARHGEF12	cis	cerebellum	SCAN
rs12364701	TMEM136	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120196400-120206400	Weak transcription	Gastric	stomach
2	chr11:120196800-120205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:120196800-120205800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:120196800-120206200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:120197200-120205800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:120197200-120205800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:120197600-120205800	Weak transcription	Liver	Liver
8	chr11:120197800-120205600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:120198000-120205200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:120198000-120205600	Enhancers	Hela-S3	cervix
11	chr11:120198200-120205600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr11:120198200-120205600	Weak transcription	HepG2	liver
13	chr11:120198400-120204000	Weak transcription	GM12878-XiMat	blood
14	chr11:120198400-120204600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr11:120198400-120205600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr11:120198400-120205800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr11:120198400-120206400	Weak transcription	Lung	lung
18	chr11:120198400-120206400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:120199400-120205200	Weak transcription	Colon Smooth Muscle	Colon
20	chr11:120199600-120205800	Weak transcription	Right Atrium	heart
21	chr11:120200600-120203800	Strong transcription	Brain Germinal Matrix	brain
22	chr11:120201000-120204800	Enhancers	HMEC	breast
23	chr11:120201200-120205800	Weak transcription	Brain Angular Gyrus	brain
24	chr11:120201200-120206400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:120201200-120206400	Weak transcription	Spleen	Spleen
26	chr11:120201400-120204400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr11:120201400-120205600	Weak transcription	Adipose Nuclei	Adipose
28	chr11:120201400-120205800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:120201400-120205800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:120201600-120204000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:120201600-120204800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:120201600-120205600	Weak transcription	Fetal Brain Male	brain
33	chr11:120201600-120205600	Enhancers	HSMMtube	muscle
34	chr11:120201600-120205600	Enhancers	HUVEC	blood vessel
35	chr11:120201800-120204000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr11:120201800-120205600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:120201800-120205600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:120201800-120205800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr11:120202000-120204600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr11:120202000-120205600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr11:120202000-120205600	Weak transcription	Fetal Intestine Large	intestine
42	chr11:120202000-120205600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr11:120202000-120205800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr11:120202200-120204600	Enhancers	NHLF	lung
45	chr11:120202200-120205200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:120202200-120205600	Enhancers	NHDF-Ad	bronchial
47	chr11:120202200-120205800	Weak transcription	Left Ventricle	heart
48	chr11:120202400-120203800	Weak transcription	Brain Hippocampus Middle	brain
49	chr11:120202400-120204400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:120202400-120204600	Enhancers	HSMM	muscle

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