Variant report

Variant	rs2576040
Chromosome Location	chr18:44582027-44582028
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:44580930..44582720-chr18:44583404..44586323,2	K562	blood:

Variant related genes	Relation type
ENSG00000167216	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10070	0.92[CEU][hapmap]
rs10502879	0.81[CEU][hapmap]
rs10853545	0.82[GIH][hapmap]
rs10853547	0.82[GIH][hapmap]
rs11660085	0.96[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12386118	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1465722	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1539878	0.82[GIH][hapmap]
rs1970668	0.96[CEU][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2010834	0.82[GIH][hapmap]
rs2032215	0.82[GIH][hapmap]
rs2156050	0.82[GIH][hapmap]
rs2164104	0.96[CEU][hapmap]
rs2187091	0.80[EUR][1000 genomes]
rs2187092	0.82[GIH][hapmap]
rs2247021	0.83[GIH][hapmap];0.83[TSI][hapmap]
rs2247221	0.83[GIH][hapmap];0.83[TSI][hapmap]
rs2571000	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571019	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2571021	0.83[GIH][hapmap];0.96[TSI][hapmap]
rs2571028	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2571030	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs2571034	0.83[GIH][hapmap]
rs2576035	0.83[GIH][hapmap]
rs2576036	0.83[GIH][hapmap];0.91[TSI][hapmap]
rs2576037	0.83[GIH][hapmap]
rs2576042	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576050	0.96[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs477826	0.92[CEU][hapmap]
rs4890343	0.96[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4890698	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs4890700	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs501062	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs501882	0.92[CEU][hapmap]
rs504668	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs513775	0.92[CEU][hapmap]
rs530205	0.92[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs553456	0.82[GIH][hapmap]
rs578451	0.92[CEU][hapmap]
rs590923	0.92[CEU][hapmap]
rs593340	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs616900	0.92[CEU][hapmap]
rs626217	0.82[GIH][hapmap]
rs641366	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs642897	0.82[GIH][hapmap]
rs644731	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs646128	0.92[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs649076	0.82[GIH][hapmap]
rs6507709	0.82[GIH][hapmap]
rs658756	0.82[GIH][hapmap]
rs680018	0.92[CEU][hapmap]
rs7233515	0.83[GIH][hapmap]
rs7240239	0.82[GIH][hapmap]
rs7244778	0.82[GIH][hapmap]
rs8086286	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs8094654	0.96[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8095373	0.82[GIH][hapmap]
rs8096263	0.80[EUR][1000 genomes]
rs892586	0.96[CEU][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9304336	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs9947131	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9948103	0.80[EUR][1000 genomes]
rs9954336	0.92[CEU][hapmap]
rs9959877	0.80[EUR][1000 genomes]
rs9960463	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv909609	chr18:44513071-44597092	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv2282	chr18:44547638-44590333	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv909610	chr18:44549455-44602249	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv909611	chr18:44560875-44614090	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1057235	chr18:44564162-44595809	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1067278	chr18:44564162-44629283	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2576040	ST8SIA5	cis	cerebellum	SCAN
rs2576040	ST8SIA5	cis	lymphoblastoid	seeQTL
rs2576040	PIAS2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44577400-44594000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr18:44579800-44630200	Weak transcription	Right Ventricle	heart
3	chr18:44580600-44595400	Weak transcription	H9 Cell Line	embryonic stem cell

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