Variant report

Variant	rs3014253
Chromosome Location	chr1:227548499-227548500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227545277..227548710-chr1:227557152..227561579,4	K562	blood:
2	chr1:227502250..227505928-chr1:227547015..227550007,4	K562	blood:
3	chr1:227539859..227541610-chr1:227547755..227549501,2	K562	blood:
4	chr1:227542971..227547040-chr1:227548442..227550941,4	K562	blood:
5	chr1:227502375..227508330-chr1:227544221..227551404,10	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10495255	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs12035986	1.00[JPT][hapmap]
rs12044287	0.94[JPT][hapmap]
rs12137591	0.94[JPT][hapmap]
rs12565871	0.94[JPT][hapmap]
rs2953637	0.85[ASN][1000 genomes]
rs2953638	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[ASN][1000 genomes]
rs2953641	0.94[ASN][1000 genomes]
rs2953643	0.96[ASN][1000 genomes]
rs2953645	0.96[ASN][1000 genomes]
rs2953650	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2953652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2953653	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2953655	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2953656	0.96[ASN][1000 genomes]
rs3014252	0.93[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[ASN][1000 genomes]
rs3014256	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3014263	0.96[ASN][1000 genomes]
rs3014267	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3014271	0.90[ASN][1000 genomes]
rs3795457	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs4339829	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4653823	0.85[EUR][1000 genomes]
rs4653824	0.85[EUR][1000 genomes]

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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3014253	CABC1	cis	cerebellum	SCAN
rs3014253	TAF1A	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227545800-227550000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227545800-227552600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:227545800-227571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:227547200-227551600	Weak transcription	K562	blood
5	chr1:227548000-227548600	Enhancers	Brain Hippocampus Middle	brain

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