Variant report

Variant	rs180408
Chromosome Location	chr12:47165323-47165324
allele	C/G
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	chr12:47165089-47165669	SK-N-SH	brain:	n/a	n/a
2	EP300	chr12:47164127-47165739	SK-N-SH	brain:	n/a	chr12:47165573-47165583
3	TCF12	chr12:47164036-47165767	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr12:47165323-47165619	SK-N-SH_RA	brain:	n/a	n/a
5	TCF12	chr12:47163975-47165772	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr12:47164008-47165768	SK-N-SH	brain:	n/a	chr12:47164482-47164498 chr12:47164486-47164493 chr12:47164485-47164493 chr12:47164486-47164493 chr12:47164485-47164495 chr12:47164486-47164493 chr12:47164486-47164495

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47164158..47166196-chr12:47171241..47173899,3	K562	blood:

Variant related genes	Relation type
SLC38A4	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11183581	0.80[EUR][1000 genomes]
rs11183589	0.81[EUR][1000 genomes]
rs11183605	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs11615446	0.81[EUR][1000 genomes]
rs12303637	0.80[EUR][1000 genomes]
rs12307895	0.87[EUR][1000 genomes]
rs12311710	0.87[EUR][1000 genomes]
rs12316767	0.87[CEU][hapmap]
rs12318216	0.80[EUR][1000 genomes]
rs12320235	0.81[EUR][1000 genomes]
rs12320632	0.80[EUR][1000 genomes]
rs12322157	0.80[EUR][1000 genomes]
rs1468970	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468971	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468972	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180409	0.87[CHB][hapmap]
rs180410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180412	0.86[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180415	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180416	0.80[CHB][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs180417	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180419	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180420	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180421	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180426	0.94[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes]
rs180427	0.82[CHB][hapmap]
rs180429	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs180430	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2080689	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287471	0.87[CEU][hapmap]
rs2408621	0.81[EUR][1000 genomes]
rs2408623	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2430916	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430920	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465595	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465614	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2543334	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2543335	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715775	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715783	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768136	0.84[EUR][1000 genomes]
rs4768750	0.80[EUR][1000 genomes]
rs56819961	0.81[EUR][1000 genomes]
rs7316285	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47149600-47165400	Weak transcription	Pancreas	Pancrea
2	chr12:47157400-47172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:47161600-47173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:47163000-47166200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:47163400-47165400	Enhancers	Fetal Lung	lung
6	chr12:47163400-47167800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr12:47163600-47165800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:47163600-47165800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:47163600-47166000	Enhancers	Adipose Nuclei	Adipose
10	chr12:47163600-47167400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:47163600-47168400	Enhancers	Hela-S3	cervix
12	chr12:47163800-47166200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:47164000-47165800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr12:47164000-47165800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr12:47164200-47165400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:47164200-47165400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr12:47164200-47165600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr12:47164200-47165600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr12:47164200-47165600	Enhancers	Rectal Smooth Muscle	rectum
20	chr12:47164200-47165800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr12:47164200-47165800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:47164200-47165800	Enhancers	NH-A	brain
23	chr12:47164200-47187800	Genic enhancers	Liver	Liver
24	chr12:47164400-47165400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:47164400-47165600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr12:47164600-47165400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr12:47164600-47165600	Weak transcription	Ovary	ovary
28	chr12:47164600-47165800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr12:47164600-47166000	Enhancers	HepG2	liver
30	chr12:47164600-47166000	Enhancers	HSMM	muscle
31	chr12:47164600-47166000	Enhancers	Osteobl	bone
32	chr12:47164600-47166800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr12:47164600-47167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:47164600-47167400	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:47164600-47167800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:47164600-47168400	Enhancers	NHDF-Ad	bronchial
37	chr12:47164600-47168400	Enhancers	NHLF	lung
38	chr12:47164800-47165400	Active TSS	Fetal Brain Male	brain
39	chr12:47164800-47165800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:47164800-47169600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr12:47165000-47165400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr12:47165000-47165400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:47165000-47168000	Weak transcription	Fetal Heart	heart
44	chr12:47165000-47169000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:47165200-47165800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr12:47165200-47165800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:47165200-47166000	Enhancers	Psoas Muscle	Psoas
48	chr12:47165200-47166000	Flanking Active TSS	HSMMtube	muscle
49	chr12:47165200-47169400	Enhancers	Fetal Muscle Leg	muscle
50	chr12:47165200-47187200	Weak transcription	Fetal Kidney	kidney

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