Variant report

Variant	rs4304839
Chromosome Location	chr12:20703492-20703493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:20703341-20703513	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:20702878..20705929-chr16:33961732..33966726,6	K562	blood:
2	chr12:20702945..20705941-chr21:9824136..9826068,2	MCF-7	breast:
3	chr12:20702883..20704468-chr21:9825694..9828983,5	MCF-7	breast:
4	chr12:20702883..20704503-chr16:33963362..33965454,3	MCF-7	breast:
5	chr1:91853063..91854565-chr12:20702914..20704451,2	K562	blood:
6	chr12:20702878..20705910-chr16:33962644..33966081,5	K562	blood:
7	chr11:85195161..85196755-chr12:20702902..20704406,2	K562	blood:
8	chr12:20702881..20704418-chr16:33963254..33964855,3	MCF-7	breast:
9	chr12:20702940..20704460-chr21:9827001..9828984,2	MCF-7	breast:
10	chr12:20702917..20705980-chr21:9825010..9828819,10	K562	blood:
11	chr1:156185131..156187864-chr12:20702974..20704505,2	K562	blood:
12	chr12:20702901..20705980-chr21:9824112..9828819,11	K562	blood:
13	chr12:20702911..20705964-chr2:133010767..133014432,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000256663	TF binding region
ENSG00000200434	Chromatin interaction
ENSG00000264063	Chromatin interaction
ENSG00000256642	Chromatin interaction
ENSG00000264462	Chromatin interaction
ENSG00000202174	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10770666	0.88[ASN][1000 genomes]
rs10770668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10841554	0.84[CEU][hapmap]
rs10841555	0.80[ASN][1000 genomes]
rs10841556	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10841557	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10841561	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[EUR][1000 genomes]
rs11045285	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11045288	0.86[ASN][1000 genomes]
rs11045291	0.86[ASN][1000 genomes]
rs11045298	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11045299	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11045301	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12425566	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12580359	0.90[ASN][1000 genomes]
rs12813387	0.83[CEU][hapmap]
rs12820858	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12822341	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2311	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs35340841	0.89[ASN][1000 genomes]
rs35466062	0.82[ASN][1000 genomes]
rs35529204	0.88[ASN][1000 genomes]
rs35574173	0.82[ASN][1000 genomes]
rs4353322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4502032	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4561252	0.81[CHB][hapmap]
rs4598713	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4627131	0.99[ASN][1000 genomes]
rs4762969	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4762970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4762971	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]
rs55975172	0.94[ASN][1000 genomes]
rs58362327	0.90[ASN][1000 genomes]
rs6487100	0.88[ASN][1000 genomes]
rs6487101	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6487105	0.85[CHB][hapmap]
rs67369958	0.86[ASN][1000 genomes]
rs7131827	0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7303620	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73075154	0.81[ASN][1000 genomes]
rs73075175	0.91[ASN][1000 genomes]
rs7308418	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7316700	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7487165	0.80[JPT][hapmap]
rs7488735	0.85[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7488869	0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7959560	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[TSI][hapmap]
rs7965577	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs7969959	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.88[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
rs4304839	ST8SIA1	cis	cerebellum	SCAN
rs4304839	PDE3A	cis	cerebellum	SCAN

Chromatin state (count:35 , 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	chr12:20699600-20704200	Weak transcription	Aorta	Aorta
7	chr12:20700200-20704200	Weak transcription	Right Atrium	heart
8	chr12:20700400-20704200	Weak transcription	Fetal Intestine Small	intestine
9	chr12:20700600-20704200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:20700800-20704200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:20701200-20704200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:20701400-20704200	Weak transcription	Fetal Brain Female	brain
13	chr12:20701800-20704200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:20701800-20704200	Weak transcription	Adipose Nuclei	Adipose
15	chr12:20701800-20704200	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:20701800-20704200	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:20702000-20704200	Weak transcription	Brain Angular Gyrus	brain
18	chr12:20702000-20704200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:20702000-20704200	Weak transcription	NHDF-Ad	bronchial
20	chr12:20702200-20704200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:20702200-20704200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:20702200-20704200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:20702200-20704200	Weak transcription	HUVEC	blood vessel
24	chr12:20702400-20704200	Weak transcription	Fetal Brain Male	brain
25	chr12:20702600-20704200	Weak transcription	Brain Substantia Nigra	brain
26	chr12:20702600-20704200	Weak transcription	Fetal Lung	lung
27	chr12:20702600-20704200	Weak transcription	A549	lung
28	chr12:20702600-20704200	Weak transcription	Osteobl	bone
29	chr12:20703000-20704200	Weak transcription	Brain Germinal Matrix	brain
30	chr12:20703000-20704200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:20703000-20704200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:20703200-20704200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:20703200-20704200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:20703200-20704200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:20703200-20704200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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