Variant report

Variant	rs11183609
Chromosome Location	chr12:47167837-47167838
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	TEAD4	chr12:47167612-47168278	SK-N-SH	brain:	n/a	chr12:47167938-47167947
2	POLR2A	chr12:47167335-47168192	SK-N-SH	brain:	n/a	n/a
3	NR3C1	chr12:47167768-47168311	ECC-1	luminal epithelium:	n/a	chr12:47168029-47168050 chr12:47168032-47168046 chr12:47168212-47168238 chr12:47168212-47168238 chr12:47168031-47168047
4	GATA3	chr12:47167339-47168548	SK-N-SH	brain:	n/a	n/a
5	MAX	chr12:47167735-47168424	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr12:47167550-47168561	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr12:47167526-47168515	SK-N-SH	brain:	n/a	n/a
8	EP300	chr12:47167491-47168320	SK-N-SH	brain:	n/a	n/a
9	NFIC	chr12:47167488-47168322	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr12:47167272-47168461	SK-N-SH	brain:	n/a	chr12:47167321-47167330
11	IRF3	chr12:47167796-47168463	Hela-S3	cervix:	n/a	chr12:47168443-47168453
12	PBX3	chr12:47167558-47168321	SK-N-SH	brain:	n/a	n/a
13	MYC	chr12:47167816-47168016	MCF10A-Er-Src	breast:	n/a	n/a
14	JUN	chr12:47167770-47168335	Hela-S3	cervix:	n/a	n/a
15	FOSL2	chr12:47167614-47168316	SK-N-SH	brain:	n/a	n/a
16	NR3C1	chr12:47167750-47168269	A549	lung:	n/a	chr12:47168029-47168050 chr12:47168032-47168046 chr12:47168212-47168238 chr12:47168212-47168238 chr12:47168031-47168047
17	POLR2A	chr12:47167752-47167940	MCF10A-Er-Src	breast:	n/a	n/a
18	CEBPB	chr12:47167772-47168302	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr12:47167689-47168176	MCF10A-Er-Src	breast:	n/a	n/a
20	CEBPB	chr12:47167819-47168114	IMR90	lung:	n/a	n/a
21	JUND	chr12:47167683-47168139	Hela-S3	cervix:	n/a	n/a
22	NR3C1	chr12:47167745-47168214	ECC-1	luminal epithelium:	n/a	chr12:47168029-47168050 chr12:47168032-47168046 chr12:47168031-47168047
23	JUND	chr12:47167546-47168231	SK-N-SH	brain:	n/a	n/a
24	FOS	chr12:47167791-47168094	MCF10A-Er-Src	breast:	n/a	n/a
25	TCF12	chr12:47167587-47168559	SK-N-SH	brain:	n/a	n/a
26	JUND	chr12:47167502-47168323	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47167274..47169486-chr12:47171150..47173434,2	K562	blood:

Variant related genes	Relation type
SLC38A4	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11609070	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11615573	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12313427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12316848	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2287472	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4768133	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7297226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv826361	chr12:47159545-47200894	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47157400-47172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:47161600-47173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:47163600-47168400	Enhancers	Hela-S3	cervix
4	chr12:47164200-47187800	Genic enhancers	Liver	Liver
5	chr12:47164600-47168400	Enhancers	NHDF-Ad	bronchial
6	chr12:47164600-47168400	Enhancers	NHLF	lung
7	chr12:47164800-47169600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:47165000-47168000	Weak transcription	Fetal Heart	heart
9	chr12:47165000-47169000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:47165200-47169400	Enhancers	Fetal Muscle Leg	muscle
11	chr12:47165200-47187200	Weak transcription	Fetal Kidney	kidney
12	chr12:47165600-47182000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:47165800-47168200	Weak transcription	Left Ventricle	heart
14	chr12:47165800-47169600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:47166000-47168400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:47166000-47169000	Enhancers	HSMMtube	muscle
17	chr12:47166800-47168400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:47166800-47169400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:47167000-47168000	Enhancers	Fetal Brain Male	brain
20	chr12:47167000-47168400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:47167000-47168400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:47167000-47168400	Enhancers	Fetal Lung	lung
23	chr12:47167000-47168400	Enhancers	Osteobl	bone
24	chr12:47167000-47173200	Enhancers	HepG2	liver
25	chr12:47167200-47169400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr12:47167400-47168200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:47167400-47168200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:47167400-47168200	Enhancers	Colon Smooth Muscle	Colon
29	chr12:47167400-47168400	Enhancers	NH-A	brain
30	chr12:47167400-47168600	Enhancers	HSMM	muscle
31	chr12:47167600-47168000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:47167600-47168200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:47167600-47168200	Weak transcription	Pancreas	Pancrea
34	chr12:47167600-47168200	Enhancers	HMEC	breast
35	chr12:47167600-47168200	Enhancers	NHEK	skin
36	chr12:47167600-47168800	Weak transcription	Psoas Muscle	Psoas
37	chr12:47167800-47168000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:47167800-47168000	Enhancers	Adipose Nuclei	Adipose
39	chr12:47167800-47168000	Enhancers	Placenta Amnion	Placenta Amnion
40	chr12:47167800-47168000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr12:47167800-47168200	Enhancers	Rectal Smooth Muscle	rectum
42	chr12:47167800-47168200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr12:47167800-47169400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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