Variant report

Variant	rs3850879
Chromosome Location	chr1:48232131-48232132
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	POLR2A	chr1:48232036-48232309	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:48231743..48234057-chr1:48237163..48240124,3	K562	blood:

Variant related genes	Relation type
ENSG00000223814	TF binding region
ENSG00000273395	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829760	chr1:48111126-48308188	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv871257	chr1:48111699-48334490	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv871175	chr1:48150309-48254782	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1001126	chr1:48164622-48320862	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1003161	chr1:48207715-48286563	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv998583	chr1:48232131-48316877	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3850879	LOC388630	cis	cerebellum	SCAN
rs3850879	BEST4	cis	parietal	SCAN
rs3850879	BEST4	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:48215400-48236200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:48218600-48239800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:48225400-48234000	Enhancers	Right Atrium	heart
4	chr1:48225600-48237000	Weak transcription	Fetal Intestine Large	intestine
5	chr1:48227000-48233600	Weak transcription	Hela-S3	cervix
6	chr1:48228000-48238800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:48228200-48238000	Weak transcription	Spleen	Spleen
8	chr1:48230000-48232200	Weak transcription	Liver	Liver
9	chr1:48230000-48233000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr1:48230400-48240000	Weak transcription	Aorta	Aorta
11	chr1:48230400-48246600	Weak transcription	Esophagus	oesophagus
12	chr1:48231200-48232600	Weak transcription	Fetal Lung	lung
13	chr1:48231200-48232800	Weak transcription	Placenta	Placenta
14	chr1:48231200-48237400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:48231200-48247000	Weak transcription	Gastric	stomach
16	chr1:48231400-48232600	Enhancers	HepG2	liver
17	chr1:48231400-48235200	Enhancers	Left Ventricle	heart
18	chr1:48231400-48236200	Enhancers	Fetal Heart	heart
19	chr1:48231600-48232200	Enhancers	Brain Germinal Matrix	brain
20	chr1:48231600-48232600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:48231600-48237000	Weak transcription	Fetal Intestine Small	intestine
22	chr1:48231800-48232600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:48231800-48234000	Enhancers	Pancreas	Pancrea
24	chr1:48232000-48235400	Enhancers	Right Ventricle	heart
25	chr1:48232000-48238600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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