Variant report

Variant	rs597123
Chromosome Location	chr8:61572983-61572984
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	RAD21	chr8:61572910-61573566	HCT-116	colon:	n/a	chr8:61573225-61573239
2	RAD21	chr8:61572908-61573428	HepG2	liver:	n/a	chr8:61573225-61573239
3	CTCF	chr8:61572878-61573660	SK-N-SH	brain:	n/a	chr8:61573209-61573217
4	SMC3	chr8:61572973-61573574	SK-N-SH	brain:	n/a	n/a
5	RAD21	chr8:61572878-61573528	SK-N-SH	brain:	n/a	chr8:61573225-61573239
6	RAD21	chr8:61572978-61573457	ECC-1	luminal epithelium:	n/a	chr8:61573225-61573239
7	CTCF	chr8:61572965-61573530	MCF-7	breast:	n/a	chr8:61573209-61573217
8	CTCF	chr8:61572961-61573413	HepG2	liver:	n/a	chr8:61573209-61573217
9	CTCF	chr8:61572899-61573571	A549	lung:	n/a	chr8:61573209-61573217
10	RAD21	chr8:61572972-61573453	A549	lung:	n/a	chr8:61573225-61573239
11	CBX3	chr8:61572980-61573630	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:61571219..61575228-chr8:61591571..61593615,3	MCF-7	breast:
2	chr8:61562433..61567496-chr8:61571905..61575539,5	K562	blood:
3	chr8:61562616..61568326-chr8:61569044..61575643,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255289	TF binding region
ENSG00000171316	Chromatin interaction
ENSG00000254869	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs2054670	0.82[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2625442	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2680296	0.89[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2680297	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2680298	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs601778	0.84[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs608740	0.89[CEU][hapmap];0.95[JPT][hapmap]
rs609264	0.90[JPT][hapmap]
rs612558	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs617434	0.85[JPT][hapmap]
rs618190	0.85[JPT][hapmap]
rs622755	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs623845	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs623917	0.88[CEU][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs625979	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs626913	0.90[JPT][hapmap]
rs629523	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs645067	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs645765	0.81[ASN][1000 genomes]
rs657718	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs658176	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs659805	0.90[ASN][1000 genomes]
rs665893	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs671204	0.95[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs671576	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs673802	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs685985	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7822621	0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530383	chr8:61431756-61605551	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv831335	chr8:61497540-61688992	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv890945	chr8:61522008-61707725	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv824657	chr8:61555227-61626758	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv824658	chr8:61561488-61612108	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv1027929	chr8:61569620-61617812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs597123	RAB2A	cis	lymphoblastoid	seeQTL
rs597123	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61567400-61573200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr8:61571400-61573400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr8:61572800-61573200	Enhancers	Primary T helper cells PMA-I stimulated	--

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