Variant report

Variant	rs625979
Chromosome Location	chr8:61559656-61559657
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:61547670..61550655-chr8:61559600..61561822,2	K562	blood:
2	chr8:61559414..61562371-chr8:61591268..61592916,2	K562	blood:
3	chr8:61559343..61568621-chr8:61588061..61597189,35	MCF-7	breast:
4	chr8:61558670..61560650-chr8:61587707..61590411,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CA8-5	chr8:61558738-61564811	NONHSAT126845

Variant related genes	Relation type
ENSG00000171316	Chromatin interaction
ENSG00000228862	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10098769	0.80[JPT][hapmap]
rs10808709	0.80[JPT][hapmap]
rs10957150	0.80[JPT][hapmap]
rs12681129	0.80[JPT][hapmap]
rs1319104	0.80[JPT][hapmap]
rs2054670	0.85[JPT][hapmap]
rs2272620	0.80[JPT][hapmap]
rs2272621	0.82[JPT][hapmap]
rs2326560	0.80[JPT][hapmap]
rs2326562	0.80[JPT][hapmap]
rs2326568	0.80[JPT][hapmap]
rs2326571	0.80[JPT][hapmap]
rs2625441	0.80[JPT][hapmap]
rs2625442	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2680296	0.92[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2680297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2680298	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2875967	0.80[JPT][hapmap]
rs2875968	0.80[JPT][hapmap]
rs2875974	0.80[JPT][hapmap]
rs2930040	0.80[JPT][hapmap]
rs2981277	0.80[JPT][hapmap]
rs3735825	0.80[JPT][hapmap]
rs3735826	0.80[JPT][hapmap]
rs41420549	0.80[JPT][hapmap]
rs595255	0.80[JPT][hapmap]
rs597123	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]
rs601778	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs603035	0.80[JPT][hapmap]
rs608740	0.92[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs609264	0.90[JPT][hapmap]
rs612558	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs615031	0.80[JPT][hapmap]
rs617434	0.85[JPT][hapmap]
rs618190	0.85[JPT][hapmap]
rs622755	0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs623845	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs623917	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]
rs625850	0.80[JPT][hapmap]
rs626913	0.90[JPT][hapmap]
rs629268	0.80[JPT][hapmap]
rs629523	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs645067	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs652422	0.80[JPT][hapmap]
rs657718	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs658176	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs659805	0.87[ASN][1000 genomes]
rs665893	0.85[JPT][hapmap]
rs669599	0.80[JPT][hapmap]
rs671204	1.00[CEU][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs671576	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs673802	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs685985	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs687351	0.80[AMR][1000 genomes]
rs687978	0.80[JPT][hapmap]
rs6987084	0.80[JPT][hapmap]
rs6995515	0.80[JPT][hapmap]
rs7013249	0.80[JPT][hapmap]
rs7413	0.80[JPT][hapmap]
rs7822621	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7829359	0.80[JPT][hapmap]
rs7839516	0.80[JPT][hapmap]
rs9643523	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs625979	RAB2	cis	multi-tissue	Pritchard
rs625979	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61554200-61564000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:61556600-61563200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr8:61558200-61560600	Weak transcription	K562	blood
4	chr8:61558400-61560600	Weak transcription	Right Ventricle	heart
5	chr8:61558600-61559800	Enhancers	Fetal Brain Male	brain
6	chr8:61558800-61563600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:61558800-61563600	Weak transcription	Left Ventricle	heart
8	chr8:61559200-61563200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr8:61559200-61563400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr8:61559200-61563600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr8:61559400-61563400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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