Variant report

Variant	rs1929846
Chromosome Location	chr6:35174642-35174643
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35168653..35170985-chr6:35173621..35175811,2	MCF-7	breast:
2	chr6:35131417..35136766-chr6:35169545..35174762,6	MCF-7	breast:
3	chr6:35173439..35175719-chr6:35204862..35206490,2	K562	blood:
4	chr6:35172932..35174925-chr6:35178829..35181429,2	K562	blood:
5	chr6:35116601..35118172-chr6:35173986..35176309,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11552398	1.00[GIH][hapmap];0.88[YRI][hapmap]
rs13207848	1.00[GIH][hapmap]
rs13216424	0.88[GIH][hapmap]
rs16871749	1.00[GIH][hapmap]
rs16871814	1.00[GIH][hapmap]
rs1929848	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234044	1.00[GIH][hapmap]
rs2395617	0.90[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756856	1.00[GIH][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap]
rs4713842	0.82[MEX][hapmap]
rs4713843	0.82[MEX][hapmap]
rs4713844	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457815	1.00[CHB][hapmap]
rs6906666	1.00[GIH][hapmap]
rs6919534	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931442	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707969	1.00[MEX][hapmap]
rs729925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751726	1.00[CHB][hapmap]
rs7767150	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770619	1.00[CHB][hapmap]
rs820062	0.88[GIH][hapmap]
rs820065	0.88[GIH][hapmap]
rs820069	0.88[GIH][hapmap]
rs820095	1.00[GIH][hapmap]
rs820099	0.88[GIH][hapmap]
rs820101	0.88[GIH][hapmap]
rs9394282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9658077	1.00[CHB][hapmap]
rs9658081	1.00[CHB][hapmap]
rs9658085	1.00[CHB][hapmap]
rs9658089	1.00[CHD][hapmap]
rs9658118	1.00[CHD][hapmap]
rs9658119	1.00[CHB][hapmap];1.00[CHD][hapmap]

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	esv3428128	chr6:35150524-35225843	Bivalent Enhancer Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1929846	TCP11	cis	lymphoblastoid	seeQTL
rs1929846	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35168200-35176200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:35169800-35175000	Enhancers	Osteobl	bone
3	chr6:35171400-35177600	Weak transcription	Fetal Heart	heart
4	chr6:35173400-35174800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:35173800-35174800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:35174000-35174800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:35174200-35174800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:35174400-35174800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:35174600-35180600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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