Variant report

Variant	rs17649609
Chromosome Location	chr1:171738453-171738454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171710037..171714996-chr1:171734843..171738629,6	MCF-7	breast:
2	chr1:171710965..171713390-chr1:171737904..171740813,3	MCF-7	breast:
3	chr1:171730299..171731843-chr1:171736543..171739308,2	K562	blood:
4	chr1:171709564..171713750-chr1:171736602..171743117,7	K562	blood:
5	chr1:171735538..171739658-chr1:171748409..171750930,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117533	Chromatin interaction
ENSG00000010165	Chromatin interaction
ENSG00000236741	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1045456	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10489252	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[EUR][1000 genomes]
rs10913683	0.98[EUR][1000 genomes]
rs10913684	0.98[EUR][1000 genomes]
rs12091786	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12565176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567851	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12730717	0.98[EUR][1000 genomes]
rs12742601	0.98[EUR][1000 genomes]
rs12750330	0.87[EUR][1000 genomes]
rs12753043	0.98[EUR][1000 genomes]
rs17596025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17596081	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17650310	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17650340	0.98[EUR][1000 genomes]
rs17657363	0.90[EUR][1000 genomes]
rs1801898	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2143369	0.98[EUR][1000 genomes]
rs2181216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2223602	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs2232807	0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs2232813	0.98[EUR][1000 genomes]
rs2232819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2232824	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2232825	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2294718	1.00[CEU][hapmap]
rs236894	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs236897	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs236898	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs236899	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs236900	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs236907	1.00[CEU][hapmap]
rs34320898	0.98[EUR][1000 genomes]
rs34627492	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35249022	0.96[EUR][1000 genomes]
rs35400839	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35631282	0.98[EUR][1000 genomes]
rs35674909	0.98[EUR][1000 genomes]
rs35882887	0.98[EUR][1000 genomes]
rs35930163	0.98[EUR][1000 genomes]
rs36080557	0.98[EUR][1000 genomes]
rs3891278	0.98[EUR][1000 genomes]
rs55732843	0.90[EUR][1000 genomes]
rs56365362	0.98[EUR][1000 genomes]
rs56377810	0.98[EUR][1000 genomes]
rs61807979	0.98[EUR][1000 genomes]
rs6656852	0.98[EUR][1000 genomes]
rs6674364	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6675708	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6681322	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6689125	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695933	0.98[EUR][1000 genomes]
rs7522582	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs7536142	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17649609	DUSP27	cis	parietal	SCAN
rs17649609	METTL13	cis	cerebellum	SCAN
rs17649609	PIGC	cis	parietal	SCAN
rs17649609	VAMP4	cis	cerebellum	SCAN
rs17649609	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs17649609	RHOA	trans	parietal	SCAN
rs17649609	MAEL	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171735200-171738600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:171736600-171738600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr1:171737400-171738600	Enhancers	Adipose Nuclei	Adipose
4	chr1:171737600-171739200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:171737800-171739200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:171737800-171739200	Enhancers	Fetal Brain Male	brain
7	chr1:171737800-171739200	Enhancers	Fetal Brain Female	brain
8	chr1:171738400-171739400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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