Variant report

Variant	rs12340744
Chromosome Location	chr9:79120298-79120299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79118137..79121617-chr9:79133678..79136692,4	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10116826	1.00[EUR][1000 genomes]
rs10117138	1.00[EUR][1000 genomes]
rs10119188	1.00[EUR][1000 genomes]
rs10120866	1.00[EUR][1000 genomes]
rs10120887	1.00[EUR][1000 genomes]
rs10123386	1.00[EUR][1000 genomes]
rs10123459	1.00[EUR][1000 genomes]
rs10125699	1.00[EUR][1000 genomes]
rs11144936	1.00[EUR][1000 genomes]
rs12000462	1.00[EUR][1000 genomes]
rs12003549	1.00[EUR][1000 genomes]
rs12343728	1.00[EUR][1000 genomes]
rs12349066	1.00[EUR][1000 genomes]
rs12352019	1.00[EUR][1000 genomes]
rs17062615	1.00[EUR][1000 genomes]
rs17062617	1.00[EUR][1000 genomes]
rs17062620	1.00[EUR][1000 genomes]
rs28607333	1.00[EUR][1000 genomes]
rs28803171	1.00[EUR][1000 genomes]
rs35340990	1.00[EUR][1000 genomes]
rs4606124	1.00[EUR][1000 genomes]
rs56914572	1.00[EUR][1000 genomes]
rs57011789	1.00[EUR][1000 genomes]
rs7027657	1.00[EUR][1000 genomes]
rs7032475	1.00[EUR][1000 genomes]
rs7874984	1.00[EUR][1000 genomes]
rs9314852	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv893480	chr9:79115844-79222584	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv437089	chr9:79116975-79139590	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12340744	SIX3	trans	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79093400-79142800	Weak transcription	Fetal Stomach	stomach
2	chr9:79112000-79120400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:79114400-79122800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:79115000-79122600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:79115200-79120400	Strong transcription	Fetal Intestine Large	intestine
6	chr9:79115400-79120400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr9:79115600-79120800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:79116600-79121200	Weak transcription	Esophagus	oesophagus
9	chr9:79117400-79120400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:79118200-79120600	Strong transcription	HSMM	muscle
11	chr9:79118400-79121000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:79118400-79122800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:79118600-79120400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:79118600-79120400	Weak transcription	Lung	lung
15	chr9:79118600-79120600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr9:79118600-79120600	Weak transcription	Spleen	Spleen
17	chr9:79118600-79122000	Weak transcription	Stomach Mucosa	stomach
18	chr9:79118600-79122600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:79118600-79123200	Strong transcription	Osteobl	bone
20	chr9:79118600-79126200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:79118600-79134200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:79118800-79120400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr9:79118800-79120400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:79118800-79120400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:79118800-79120400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:79118800-79120600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:79118800-79120600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:79118800-79121200	Weak transcription	Colonic Mucosa	Colon
29	chr9:79118800-79121400	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr9:79118800-79121400	Weak transcription	NH-A	brain
31	chr9:79118800-79124600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:79118800-79125200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr9:79118800-79125200	Weak transcription	NHDF-Ad	bronchial
34	chr9:79118800-79127600	Weak transcription	HSMMtube	muscle
35	chr9:79118800-79136400	Weak transcription	Gastric	stomach
36	chr9:79118800-79145800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr9:79119000-79120600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr9:79119000-79120600	Weak transcription	Fetal Muscle Leg	muscle
39	chr9:79119000-79120800	Weak transcription	GM12878-XiMat	blood
40	chr9:79119000-79122400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr9:79119000-79123000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:79119000-79123200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr9:79119000-79125200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:79119200-79120800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr9:79119200-79121400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:79119200-79124800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr9:79119200-79125200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:79119200-79125200	Weak transcription	NHLF	lung
49	chr9:79119200-79127800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr9:79119200-79134000	Weak transcription	Fetal Intestine Small	intestine

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