Variant report

Variant	rs4972516
Chromosome Location	chr2:173547381-173547382
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	USF1	chr2:173547220-173547381	HepG2	liver:	n/a	chr2:173547299-173547310
2	USF1	chr2:173547135-173547501	H1-hESC	embryonic stem cell:	n/a	chr2:173547299-173547310
3	MAX	chr2:173547171-173547389	H1-hESC	embryonic stem cell:	n/a	n/a
4	USF1	chr2:173547101-173547453	ECC-1	luminal epithelium:	n/a	chr2:173547299-173547310

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173419077..173420635-chr2:173545437..173548321,2	K562	blood:
2	chr2:173545996..173547496-chr20:31169741..31172058,2	K562	blood:

Variant related genes	Relation type
RAPGEF4-AS1	TF binding region
ENSG00000228156	Chromatin interaction
ENSG00000152256	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10166107	0.90[AFR][1000 genomes]
rs10190099	0.81[AFR][1000 genomes]
rs10198546	0.82[AFR][1000 genomes]
rs10205076	0.91[AFR][1000 genomes]
rs10205126	0.97[AFR][1000 genomes]
rs11887904	0.89[AFR][1000 genomes]
rs11902830	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12615889	0.85[ASN][1000 genomes]
rs12622335	0.84[ASN][1000 genomes]
rs12622834	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13384307	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13384609	0.98[AFR][1000 genomes]
rs13387816	0.95[AFR][1000 genomes]
rs13417913	0.82[AFR][1000 genomes]
rs13422388	0.98[AFR][1000 genomes]
rs13425350	0.98[AFR][1000 genomes]
rs16860794	0.85[ASN][1000 genomes]
rs16860795	0.85[ASN][1000 genomes]
rs16860796	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16860798	0.85[ASN][1000 genomes]
rs16860809	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2054162	0.81[ASN][1000 genomes]
rs2054163	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2084731	0.85[ASN][1000 genomes]
rs2084732	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs28670307	0.98[AFR][1000 genomes]
rs4313941	0.84[ASN][1000 genomes]
rs4470304	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4972514	0.85[ASN][1000 genomes]
rs4972515	0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4972849	0.85[ASN][1000 genomes]
rs4972850	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4972851	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs59103702	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59648896	0.88[AFR][1000 genomes]
rs61556691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62169319	0.91[AFR][1000 genomes]
rs6716527	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733953	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs733331	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7590282	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173539600-173554200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:173546200-173549400	Weak transcription	Colon Smooth Muscle	Colon

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