Variant report

Variant	rs12668958
Chromosome Location	chr7:128938239-128938240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128858109..128859536-chr7:128937762..128939140,17	K562	blood:
2	chr7:128864334..128864911-chr7:128937875..128938561,2	MCF-7	breast:
3	chr7:128862235..128863197-chr7:128937895..128938804,2	K562	blood:
4	chr7:128858254..128859049-chr7:128938074..128938750,3	MCF-7	breast:
5	chr7:128850005..128850635-chr7:128937801..128938311,2	K562	blood:
6	chr7:128858083..128859103-chr7:128937805..128938973,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158467	Chromatin interaction
ENSG00000128602	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1000676	1.00[ASW][hapmap];0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap]
rs10248810	0.90[JPT][hapmap]
rs10954226	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs10954230	0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs11979476	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs12112374	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs12532192	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12534372	0.95[JPT][hapmap]
rs12540568	1.00[ASW][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap]
rs12667132	0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs1526900	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1559486	0.85[JPT][hapmap]
rs1880854	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs2694572	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs34022136	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34284898	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35305688	0.82[EUR][1000 genomes]
rs4460315	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4728163	1.00[ASW][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.96[MKK][hapmap]
rs4728164	1.00[ASW][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap]
rs4731568	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4731569	0.93[ASN][1000 genomes]
rs4731572	0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs4731575	0.95[JPT][hapmap]
rs6966595	0.85[JPT][hapmap]
rs6980385	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs721691	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7788327	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs7800983	0.91[ASN][1000 genomes]
rs822038	0.85[JPT][hapmap]
rs822040	0.85[JPT][hapmap]
rs9649530	0.93[ASN][1000 genomes]
rs9649531	0.93[ASN][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	nsv525482	chr7:128890812-129045191	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv3331483	chr7:128918442-129082887	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12668958	KCP	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128912200-128947000	Weak transcription	Pancreas	Pancrea
2	chr7:128913200-128940800	Weak transcription	Aorta	Aorta
3	chr7:128915000-128962600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:128920000-128951600	Weak transcription	Primary T cells from cord blood	blood
5	chr7:128925800-128947600	Weak transcription	Ovary	ovary
6	chr7:128929200-128963800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:128932800-128938800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:128935600-128946400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:128935800-128938400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:128936800-128938600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:128938000-128938600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr7:128938000-128938600	Enhancers	Skeletal Muscle Male	skeletal muscle

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