Variant report

Variant	rs6722478
Chromosome Location	chr2:39149483-39149484
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38975236..38979856-chr2:39147860..39151897,5	K562	blood:
2	chr2:39106402..39108515-chr2:39149048..39151113,2	MCF-7	breast:
3	chr2:39145069..39147790-chr2:39148985..39151142,2	MCF-7	breast:
4	chr2:39147727..39150227-chr2:39155221..39157065,2	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000214694	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10495883	1.00[GIH][hapmap]
rs13429447	1.00[EUR][1000 genomes]
rs1376461	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17023214	1.00[JPT][hapmap]
rs1901290	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2373466	1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs2373472	0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs3099947	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3099953	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3099997	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3112138	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs3112155	0.92[AMR][1000 genomes]
rs3112158	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs3112160	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs3112164	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3112174	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3112176	0.82[JPT][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3112177	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56322480	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57884089	0.92[ASN][1000 genomes]
rs58412684	1.00[ASN][1000 genomes]
rs58645810	1.00[ASN][1000 genomes]
rs59788371	1.00[ASN][1000 genomes]
rs60406386	1.00[ASN][1000 genomes]
rs61393528	1.00[ASN][1000 genomes]
rs6544182	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6712917	1.00[JPT][hapmap]
rs6722176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748000	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72916821	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7368897	1.00[JPT][hapmap]
rs73930373	1.00[ASN][1000 genomes]
rs73930374	1.00[ASN][1000 genomes]
rs73930378	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7571935	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605183	1.00[ASN][1000 genomes]
rs921433	1.00[GIH][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6722478	SOS1	cis	lymphoblastoid	seeQTL
rs6722478	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39110200-39186800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:39139600-39150000	Weak transcription	Psoas Muscle	Psoas
3	chr2:39142000-39150000	Weak transcription	Right Ventricle	heart
4	chr2:39143000-39151000	Weak transcription	Brain Angular Gyrus	brain
5	chr2:39143800-39164600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:39145200-39149800	Weak transcription	Brain Anterior Caudate	brain
7	chr2:39145800-39172800	Weak transcription	Lung	lung
8	chr2:39147000-39166600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:39147800-39150400	Enhancers	HepG2	liver
10	chr2:39149000-39164800	Weak transcription	Ovary	ovary

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