Variant report

Variant	rs11168740
Chromosome Location	chr12:49180633-49180634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr12:49180403-49180884	MCF-7	breast:	n/a	chr12:49180526-49180541
2	MXI1	chr12:49180368-49183259	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49179602..49181773-chr12:49197914..49199450,2	K562	blood:
2	chr12:49074389..49076545-chr12:49180456..49183753,3	MCF-7	breast:
3	chr12:49180246..49182305-chr12:49186657..49190531,5	MCF-7	breast:
4	chr12:49178102..49185044-chr12:49204782..49211867,14	MCF-7	breast:
5	chr12:49180478..49186692-chr12:49206898..49214052,14	MCF-7	breast:
6	chr12:49160841..49162680-chr12:49178634..49181167,2	MCF-7	breast:
7	chr12:49165064..49172292-chr12:49177951..49185171,13	MCF-7	breast:

No data

Variant related genes	Relation type
ADCY6	TF binding region
ENSG00000257660	TF binding region
ENSG00000139620	Chromatin interaction
ENSG00000264201	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000174233	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10875874	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875875	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168732	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11168733	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11168734	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168736	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168737	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168738	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168739	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168742	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs12306165	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs12307769	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12314663	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319012	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35468640	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35801460	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729969	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs3729980	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MKK][hapmap]
rs3730069	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3730070	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3730072	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3730074	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs68003719	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132180	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7300155	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs7307701	0.86[ASN][1000 genomes]
rs7975385	1.00[CHD][hapmap]
rs9668292	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804777	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11168740	CACNB3	cis	parietal	SCAN
rs11168740	ARID2	cis	parietal	SCAN
rs11168740	CACNB3	cis	cerebellum	SCAN
rs11168740	RAPGEF3	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49159400-49181000	Weak transcription	Small Intestine	intestine
2	chr12:49168400-49181400	Weak transcription	Fetal Kidney	kidney
3	chr12:49169800-49181200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:49170000-49180800	Weak transcription	Brain Anterior Caudate	brain
5	chr12:49171200-49180800	Weak transcription	Brain Angular Gyrus	brain
6	chr12:49172200-49181600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:49172400-49180800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:49172400-49181200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:49174600-49180800	Weak transcription	HSMM	muscle
10	chr12:49174600-49181000	Weak transcription	HSMMtube	muscle
11	chr12:49174800-49181200	Weak transcription	Brain Substantia Nigra	brain
12	chr12:49174800-49181200	Weak transcription	HUVEC	blood vessel
13	chr12:49175800-49180800	Weak transcription	NH-A	brain
14	chr12:49175800-49181600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:49176200-49180800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:49176200-49181200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:49176400-49181000	Weak transcription	NHEK	skin
18	chr12:49176600-49180800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:49177000-49181000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:49177000-49181000	Weak transcription	NHLF	lung
21	chr12:49177200-49181000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:49177200-49181000	Enhancers	Left Ventricle	heart
23	chr12:49177400-49180800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:49177400-49180800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:49177400-49180800	Weak transcription	Fetal Intestine Large	intestine
26	chr12:49177400-49180800	Weak transcription	Placenta	Placenta
27	chr12:49177400-49180800	Weak transcription	Gastric	stomach
28	chr12:49177400-49180800	Weak transcription	A549	lung
29	chr12:49177400-49181000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:49177400-49181000	Weak transcription	Liver	Liver
31	chr12:49177600-49180800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:49177600-49180800	Weak transcription	Fetal Intestine Small	intestine
33	chr12:49177600-49180800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:49177600-49181000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:49178600-49181000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr12:49178800-49181000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:49178800-49181000	Enhancers	Right Ventricle	heart
38	chr12:49179600-49180800	Flanking Active TSS	Fetal Heart	heart
39	chr12:49179600-49181000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:49179600-49181000	Enhancers	Brain Germinal Matrix	brain
41	chr12:49179600-49181000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr12:49179600-49181600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:49179800-49180800	Enhancers	Esophagus	oesophagus
44	chr12:49179800-49180800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr12:49179800-49181000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:49179800-49181000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:49179800-49181000	Enhancers	Aorta	Aorta
48	chr12:49179800-49181000	Enhancers	Ovary	ovary
49	chr12:49179800-49181000	Enhancers	Pancreas	Pancrea
50	chr12:49179800-49181200	Enhancers	NHDF-Ad	bronchial

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