Variant report

Variant	rs4762971
Chromosome Location	chr12:20701230-20701231
allele	A/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	CTCF	chr12:20700655-20703062	A549	lung:	n/a	chr12:20702239-20702252 chr12:20702242-20702250 chr12:20702238-20702254 chr12:20702237-20702255
2	GATA3	chr12:20701130-20702443	SK-N-SH	brain:	n/a	chr12:20701767-20701774 chr12:20701763-20701779 chr12:20701767-20701774 chr12:20701763-20701779 chr12:20701706-20701715 chr12:20701766-20701776 chr12:20701767-20701776 chr12:20701407-20701423 chr12:20701760-20701781 chr12:20701767-20701774
3	EP300	chr12:20701181-20701405	SK-N-SH_RA	brain:	n/a	n/a
4	TCF12	chr12:20700577-20701530	A549	lung:	n/a	chr12:20701113-20701121
5	RAD21	chr12:20701082-20702638	SK-N-SH	brain:	n/a	chr12:20702239-20702253 chr12:20702245-20702252

Variant related genes	Relation type
ENSG00000256663	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10770666	0.85[ASN][1000 genomes]
rs10770668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10841554	0.84[CEU][hapmap]
rs10841556	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs10841557	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10841561	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11045285	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs11045288	0.86[ASN][1000 genomes]
rs11045291	0.83[ASN][1000 genomes]
rs11045298	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11045299	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11045301	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs12425566	0.91[CHB][hapmap]
rs12580359	0.91[ASN][1000 genomes]
rs12813387	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs12820858	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12822341	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2311	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs35340841	0.90[ASN][1000 genomes]
rs35529204	0.90[ASN][1000 genomes]
rs4304839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4353322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4502032	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4561252	0.82[CHB][hapmap]
rs4598713	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4627131	0.96[ASN][1000 genomes]
rs4762969	0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4762970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55975172	0.92[ASN][1000 genomes]
rs58362327	0.91[ASN][1000 genomes]
rs6487100	0.86[ASN][1000 genomes]
rs6487101	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6487105	0.86[CHB][hapmap]
rs67369958	0.88[ASN][1000 genomes]
rs7131827	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7303620	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73075175	0.92[ASN][1000 genomes]
rs7308418	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7316700	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7488735	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7488869	0.82[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7959560	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7965577	0.91[CHB][hapmap]
rs7969959	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1046870	chr12:20509914-20711535	Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv541409	chr12:20509914-20711535	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
5	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1054997	chr12:20682009-21292602	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4762971	PDE3A	cis	cerebellum	SCAN
rs4762971	ST8SIA1	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20673800-20704200	Weak transcription	Fetal Intestine Large	intestine
2	chr12:20688600-20704200	Weak transcription	Hela-S3	cervix
3	chr12:20692600-20704200	Weak transcription	Fetal Kidney	kidney
4	chr12:20692600-20704200	Weak transcription	Right Ventricle	heart
5	chr12:20694400-20704200	Weak transcription	Left Ventricle	heart
6	chr12:20699000-20702600	Enhancers	Osteobl	bone
7	chr12:20699400-20702200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:20699600-20704200	Weak transcription	Aorta	Aorta
9	chr12:20700200-20704200	Weak transcription	Right Atrium	heart
10	chr12:20700400-20701400	Enhancers	Fetal Brain Female	brain
11	chr12:20700400-20701600	Weak transcription	NHDF-Ad	bronchial
12	chr12:20700400-20701800	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr12:20700400-20704200	Weak transcription	Fetal Intestine Small	intestine
14	chr12:20700600-20701600	Weak transcription	Fetal Lung	lung
15	chr12:20700600-20702000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:20700600-20702200	Enhancers	HUVEC	blood vessel
17	chr12:20700600-20704200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:20700800-20701800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:20700800-20704200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:20701000-20701400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:20701000-20701600	Enhancers	A549	lung
22	chr12:20701000-20702200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:20701000-20702200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:20701200-20701800	Enhancers	Adipose Nuclei	Adipose
25	chr12:20701200-20701800	Enhancers	Colon Smooth Muscle	Colon
26	chr12:20701200-20702000	Enhancers	Brain Substantia Nigra	brain
27	chr12:20701200-20702200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:20701200-20702400	Enhancers	Fetal Brain Male	brain
29	chr12:20701200-20704200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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