Variant report

Variant	rs623917
Chromosome Location	chr8:61568210-61568211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr8:61568170-61568333	MCF10A-Er-Src	breast:	n/a	chr8:61568188-61568200

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:61563711..61566471-chr8:61567487..61569836,4	K562	blood:
2	chr8:61562515..61568989-chr8:61586860..61594946,37	MCF-7	breast:
3	chr8:61559343..61568621-chr8:61588061..61597189,35	MCF-7	breast:
4	chr8:61563005..61568398-chr8:61588453..61593214,14	K562	blood:
5	chr8:61567081..61569634-chr8:62050277..62052303,2	K562	blood:
6	chr8:61562616..61568326-chr8:61569044..61575643,11	MCF-7	breast:
7	chr8:61563620..61565259-chr8:61566551..61570060,3	K562	blood:
8	chr8:61562679..61568216-chr8:61588453..61593754,19	K562	blood:
9	chr8:61567779..61569596-chr8:61570085..61572537,2	K562	blood:

No data

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

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10090193	0.83[ASN][1000 genomes]
rs2054670	0.87[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[ASN][1000 genomes]
rs2625442	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2680296	0.94[ASW][hapmap];0.81[CEU][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2680297	0.88[CEU][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2680298	0.94[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs597123	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]
rs601778	0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs605701	0.88[ASN][1000 genomes]
rs608740	0.81[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs609264	0.94[JPT][hapmap]
rs612558	0.94[JPT][hapmap]
rs617434	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs618190	0.81[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs622755	0.86[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs623845	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs625979	0.88[CEU][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs626913	0.94[JPT][hapmap]
rs629523	0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs645067	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs645765	0.92[ASN][1000 genomes]
rs657718	0.83[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs658176	0.88[CEU][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs659805	0.82[ASN][1000 genomes]
rs665893	0.94[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[ASN][1000 genomes]
rs671204	0.87[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs671576	0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs673802	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs685985	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs686852	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7822621	0.83[CHD][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[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	nsv525495	chr8:61566655-61568210	Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs623917	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61567200-61568400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr8:61567200-61568800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr8:61567400-61573200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr8:61568200-61568400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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