Variant report

Variant	rs10878580
Chromosome Location	chr12:67594384-67594385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:67593545..67595294-chr12:67601266..67602833,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10735940	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748069	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs10748071	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs10748074	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784611	0.85[CHB][hapmap]
rs10784614	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878569	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs10878576	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878577	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878578	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878581	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878585	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176589	0.85[CHB][hapmap]
rs11176591	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs11176597	0.85[CHB][hapmap]
rs11176627	1.00[ASN][1000 genomes]
rs11176629	1.00[ASN][1000 genomes]
rs11176633	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146816	0.87[ASN][1000 genomes]
rs1370405	0.97[ASN][1000 genomes]
rs1370406	1.00[ASN][1000 genomes]
rs1569021	0.82[CHB][hapmap]
rs1595334	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595337	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657978	1.00[ASN][1000 genomes]
rs1657983	1.00[ASN][1000 genomes]
rs1866068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866255	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1866256	0.90[ASN][1000 genomes]
rs1898454	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898610	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898611	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918140	0.85[CHB][hapmap]
rs2033728	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2043800	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164746	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2870942	1.00[ASN][1000 genomes]
rs2917847	1.00[ASN][1000 genomes]
rs2917849	1.00[ASN][1000 genomes]
rs4244072	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397936	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4603385	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs4913532	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4913533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135360	0.85[CHB][hapmap]
rs775313	1.00[ASN][1000 genomes]
rs7968916	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7969451	0.85[CHB][hapmap];0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1042328	chr12:67573942-67617106	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10878580	SLC35E3	cis	cerebellum	SCAN
rs10878580	GRIP1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67593800-67595000	Enhancers	Fetal Intestine Small	intestine
2	chr12:67594200-67595600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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