Variant report

Variant	rs6802779
Chromosome Location	chr3:42772120-42772121
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	RXRA	chr3:42771857-42772283	HepG2	liver:	n/a	chr3:42772100-42772120 chr3:42772103-42772116 chr3:42772173-42772195 chr3:42772103-42772116 chr3:42772102-42772118 chr3:42772103-42772116 chr3:42772095-42772109 chr3:42772102-42772116
2	HNF4G	chr3:42771868-42772214	HepG2	liver:	n/a	chr3:42772099-42772121 chr3:42772104-42772116 chr3:42772103-42772116 chr3:42772103-42772117 chr3:42772108-42772120 chr3:42772103-42772116 chr3:42772097-42772109 chr3:42772096-42772110 chr3:42772092-42772114 chr3:42772104-42772116 chr3:42772103-42772116 chr3:42772097-42772110 chr3:42772104-42772116 chr3:42772104-42772117 chr3:42772104-42772116

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42746557..42750988-chr3:42768421..42772654,4	K562	blood:
2	chr3:42770931..42773335-chr3:42773656..42775532,2	MCF-7	breast:

Variant related genes	Relation type
CCDC13-AS1	TF binding region
ENSG00000173811	Chromatin interaction
ENSG00000244607	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs339663	1.00[MEX][hapmap]
rs35033264	1.00[MEX][hapmap]
rs4404423	1.00[MEX][hapmap]
rs6768001	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6771329	0.87[MKK][hapmap]
rs6773675	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6777653	1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6781327	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6783035	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6792887	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6794170	0.83[AFR][1000 genomes]
rs6810329	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs7610350	1.00[MEX][hapmap]
rs7612614	1.00[MEX][hapmap]
rs7648688	1.00[MEX][hapmap]
rs9755640	1.00[MEX][hapmap]
rs9882356	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42760400-42773600	Enhancers	Brain Substantia Nigra	brain
2	chr3:42763600-42773600	Enhancers	Brain Anterior Caudate	brain
3	chr3:42763600-42774800	Enhancers	Brain Angular Gyrus	brain
4	chr3:42765000-42772600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:42767600-42772600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:42767800-42774400	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:42768600-42776000	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr3:42769000-42773600	Enhancers	Brain Hippocampus Middle	brain
9	chr3:42769000-42774200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr3:42769000-42774800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:42769000-42775000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:42769600-42785600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:42769800-42773200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:42769800-42774200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:42769800-42787600	Weak transcription	Gastric	stomach
16	chr3:42770200-42772600	Enhancers	Left Ventricle	heart
17	chr3:42770200-42774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:42770600-42775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:42770800-42773400	Enhancers	Fetal Heart	heart
20	chr3:42771000-42772200	Enhancers	Psoas Muscle	Psoas
21	chr3:42771000-42774000	Enhancers	Right Ventricle	heart
22	chr3:42771000-42774200	Enhancers	Right Atrium	heart
23	chr3:42771200-42773400	Enhancers	HepG2	liver
24	chr3:42771200-42775800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:42771600-42773200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:42771800-42772200	Enhancers	Esophagus	oesophagus

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