Variant report

Variant	rs4864856
Chromosome Location	chr4:55084720-55084721
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	RAD21	chr4:55083552-55084728	SK-N-SH	brain:	n/a	chr4:55083834-55083847 chr4:55084141-55084160 chr4:55084151-55084158
2	CTCF	chr4:55083515-55085239	SK-N-SH	brain:	n/a	chr4:55084145-55084158 chr4:55084138-55084159 chr4:55084143-55084161 chr4:55084144-55084160 chr4:55084148-55084156
3	SMC3	chr4:55083587-55085210	SK-N-SH	brain:	n/a	chr4:55084145-55084159
4	POLR2A	chr4:55084011-55084998	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr4:55084030-55084871	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54795889..54796838-chr4:55083754..55084776,6	MCF-7	breast:
2	chr4:54765055..54765944-chr4:55083853..55084724,2	K562	blood:

Variant related genes	Relation type
ENSG00000242670	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11133312	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133313	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133314	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499153	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12501810	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12505054	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506783	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648347	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13139131	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17084051	0.88[AFR][1000 genomes]
rs1800809	0.89[AFR][1000 genomes]
rs1800810	0.80[AFR][1000 genomes]
rs1800812	0.88[AFR][1000 genomes]
rs2052697	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28436914	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28753397	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34521751	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4398585	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4608869	0.88[AFR][1000 genomes]
rs4635872	0.88[AFR][1000 genomes]
rs4864842	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4864855	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864858	0.83[AFR][1000 genomes]
rs4864862	0.88[AFR][1000 genomes]
rs4864863	0.86[AFR][1000 genomes]
rs60863210	0.91[AFR][1000 genomes]
rs61320297	0.94[AFR][1000 genomes]
rs6554159	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6554161	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6825018	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6845581	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6850748	0.88[AFR][1000 genomes]
rs718454	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718455	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673267	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673597	0.87[AFR][1000 genomes]
rs7673625	0.94[AFR][1000 genomes]
rs7679903	0.84[AFR][1000 genomes]
rs7681399	0.85[AFR][1000 genomes]
rs7683707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698425	0.85[AFR][1000 genomes]
rs890203	0.85[AFR][1000 genomes]
rs890206	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55084000-55085000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:55084200-55084800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:55084200-55084800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:55084200-55085200	Bivalent Enhancer	Stomach Mucosa	stomach
5	chr4:55084200-55091200	Weak transcription	Ovary	ovary
6	chr4:55084400-55085000	Enhancers	HSMM	muscle
7	chr4:55084400-55085200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:55084600-55084800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:55084600-55084800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:55084600-55084800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:55084600-55084800	Bivalent Enhancer	Brain Angular Gyrus	brain
12	chr4:55084600-55084800	Enhancers	NHLF	lung
13	chr4:55084600-55085200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:55084600-55085600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:55084600-55090600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:55084600-55091400	Weak transcription	Osteobl	bone
17	chr4:55084600-55092800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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