Variant report

Variant	rs9858223
Chromosome Location	chr3:61238218-61238219
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	chr3:61238100-61238250	HRE	kidney:	n/a	n/a
2	POLR2A	chr3:61235506-61238272	GM12891	blood:	n/a	n/a
3	CTCF	chr3:61238140-61238290	HFF-Myc	foreskin:	n/a	n/a
4	CTCF	chr3:61238120-61238270	HMF	breast:	n/a	n/a
5	E2F4	chr3:61238007-61238219	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr3:61238120-61238270	NHDF-neo	bronchial:	n/a	n/a
7	CTCF	chr3:61238120-61238270	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
FHIT	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1996958	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4315681	0.94[CEU][hapmap]
rs4688167	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6791206	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6802718	0.94[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs9817853	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs9831680	0.94[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs9873085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][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	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9858223	PRICKLE2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61237800-61239000	Weak transcription	Left Ventricle	heart
2	chr3:61237800-61239600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:61238000-61238400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:61238000-61238400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:61238000-61238400	Enhancers	Brain Anterior Caudate	brain
6	chr3:61238000-61238400	Enhancers	Fetal Muscle Leg	muscle
7	chr3:61238000-61238400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr3:61238000-61238400	Weak transcription	Thymus	Thymus
9	chr3:61238000-61238800	Enhancers	Fetal Intestine Small	intestine
10	chr3:61238000-61239200	Enhancers	HepG2	liver
11	chr3:61238000-61239400	Enhancers	Fetal Heart	heart
12	chr3:61238000-61240000	Enhancers	GM12878-XiMat	blood
13	chr3:61238000-61240200	Weak transcription	Fetal Brain Male	brain
14	chr3:61238000-61242400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:61238200-61238400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:61238200-61238400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:61238200-61238400	Enhancers	Liver	Liver
18	chr3:61238200-61238800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:61238200-61238800	Enhancers	Duodenum Mucosa	Duodenum
20	chr3:61238200-61239400	Enhancers	Dnd41	blood
21	chr3:61238200-61239400	Enhancers	HUVEC	blood vessel
22	chr3:61238200-61239600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:61238200-61239600	Enhancers	Fetal Thymus	thymus
24	chr3:61238200-61242400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:61238200-61242400	Weak transcription	Brain Substantia Nigra	brain

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