Variant report

Variant	rs2354939
Chromosome Location	chr4:48803066-48803067
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	FOXA1	chr4:48803003-48803425	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48780574..48783238-chr4:48801102..48803669,2	K562	blood:

Variant related genes	Relation type
OCIAD1	TF binding region
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10034207	0.82[YRI][hapmap]
rs10049760	0.82[YRI][hapmap]
rs10938545	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11729557	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12507475	0.85[YRI][hapmap]
rs1533511	0.82[YRI][hapmap]
rs1702799	0.82[YRI][hapmap]
rs1712762	0.82[YRI][hapmap]
rs2138866	0.82[YRI][hapmap]
rs2354942	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2465262	0.89[AFR][1000 genomes]
rs2572340	0.89[AFR][1000 genomes]
rs2572342	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2712155	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2940319	0.82[YRI][hapmap]
rs4274819	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4694905	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4695406	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6815932	0.89[AFR][1000 genomes]
rs6824209	0.89[AFR][1000 genomes]
rs6839713	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6844579	0.89[AFR][1000 genomes]
rs7654729	0.89[AFR][1000 genomes]
rs7667431	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7669831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7686458	0.92[AFR][1000 genomes]
rs7698064	0.82[YRI][hapmap]
rs7698768	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776581	0.82[YRI][hapmap]
rs776583	0.82[YRI][hapmap]
rs9994214	0.82[YRI][hapmap]
rs9998178	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48797000-48806800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:48800200-48803400	Weak transcription	Brain Anterior Caudate	brain
3	chr4:48801400-48803200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:48801400-48803200	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:48801600-48803200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:48801600-48803200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:48801600-48803200	Weak transcription	GM12878-XiMat	blood
8	chr4:48801600-48803200	Weak transcription	HUVEC	blood vessel
9	chr4:48801600-48803400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:48801600-48803400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:48801600-48803400	Weak transcription	Fetal Kidney	kidney
12	chr4:48801600-48803800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr4:48801600-48806600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:48801800-48803200	Weak transcription	Brain Substantia Nigra	brain
15	chr4:48801800-48803400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:48801800-48803400	Weak transcription	NH-A	brain
17	chr4:48801800-48806600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:48802200-48803200	Weak transcription	Brain Angular Gyrus	brain
19	chr4:48802800-48803200	Active TSS	HepG2	liver
20	chr4:48802800-48805200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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