Variant report

Variant	rs3850881
Chromosome Location	chr1:48233751-48233752
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	CTCF	chr1:48233720-48233870	HEK293	kidney:	n/a	n/a
2	POLR2A	chr1:48232602-48234163	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr1:48233700-48233850	HMEC	breast:	n/a	n/a
4	RAD21	chr1:48233676-48233875	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr1:48233740-48233890	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr1:48233747-48233918	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:48232346..48235008-chr1:48237593..48240015,2	K562	blood:
2	chr1:48231743..48234057-chr1:48237163..48240124,3	K562	blood:

Variant related genes	Relation type
ENSG00000223814	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12037415	0.84[TSI][hapmap]
rs12038078	0.84[CHD][hapmap];0.84[ASN][1000 genomes]
rs3844086	0.80[TSI][hapmap]
rs6693956	0.84[CEU][hapmap]
rs6701938	0.81[CEU][hapmap];0.82[TSI][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3850881	RNF11	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	chr1:48228000-48238800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:48228200-48238000	Weak transcription	Spleen	Spleen
7	chr1:48230400-48240000	Weak transcription	Aorta	Aorta
8	chr1:48230400-48246600	Weak transcription	Esophagus	oesophagus
9	chr1:48231200-48237400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:48231200-48247000	Weak transcription	Gastric	stomach
11	chr1:48231400-48235200	Enhancers	Left Ventricle	heart
12	chr1:48231400-48236200	Enhancers	Fetal Heart	heart
13	chr1:48231600-48237000	Weak transcription	Fetal Intestine Small	intestine
14	chr1:48231800-48234000	Enhancers	Pancreas	Pancrea
15	chr1:48232000-48235400	Enhancers	Right Ventricle	heart
16	chr1:48232000-48238600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:48232200-48234000	Enhancers	Liver	Liver
18	chr1:48232200-48237400	Enhancers	Fetal Muscle Leg	muscle
19	chr1:48232600-48234600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:48232800-48234600	Weak transcription	Brain Germinal Matrix	brain
21	chr1:48233000-48234000	Enhancers	Fetal Muscle Trunk	muscle
22	chr1:48233400-48233800	Bivalent Enhancer	Fetal Stomach	stomach
23	chr1:48233400-48234400	Weak transcription	Fetal Lung	lung
24	chr1:48233600-48234600	Weak transcription	Placenta	Placenta
25	chr1:48233600-48235200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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