Variant report

Variant	rs7783400
Chromosome Location	chr7:2894434-2894435
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2893756..2895887-chr7:2901589..2904569,2	K562	blood:
2	chr7:2890202..2892822-chr7:2894073..2897035,2	MCF-7	breast:
3	chr7:2882956..2885508-chr7:2891694..2894640,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1182143	0.82[CEU][hapmap]
rs1182155	0.95[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs1182156	0.87[ASN][1000 genomes]
rs1182174	0.84[CEU][hapmap]
rs1182183	0.81[CEU][hapmap]
rs1182198	0.81[CEU][hapmap]
rs11973498	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12700373	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13230946	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13230995	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1614791	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1623138	0.86[ASN][1000 genomes]
rs1636247	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1636249	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1636250	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1636253	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1636254	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1636255	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1636256	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1636264	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1639036	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1639040	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1639064	0.87[ASN][1000 genomes]
rs1639065	0.88[ASN][1000 genomes]
rs1639066	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1713912	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1713913	0.92[ASN][1000 genomes]
rs2107964	0.86[CEU][hapmap]
rs2527677	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2527680	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2527681	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2533867	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2533868	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2533870	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2533871	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2533877	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2533889	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2533891	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644281	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2644286	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2644293	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644300	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2644309	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71522301	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71522302	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71524003	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798485	0.81[TSI][hapmap]
rs798486	0.81[TSI][hapmap]
rs798490	0.81[TSI][hapmap]
rs798502	0.81[TSI][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	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv887313	chr7:2875420-2927120	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv887314	chr7:2875420-2944187	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7783400	GNA12	cis	lymphoblastoid	seeQTL
rs7783400	GNA12	cis	multi-tissue	Pritchard
rs7783400	GNA12	cis	Artery Tibial	GTEx
rs7783400		cis	Lymphoblastoid	GTEx
rs7783400	GNA12	cis	Nerve Tibial	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2884600-2896000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:2884600-2902800	Weak transcription	Right Ventricle	heart
3	chr7:2884800-2895800	Weak transcription	Fetal Heart	heart
4	chr7:2885000-2902000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:2890400-2895800	Weak transcription	Pancreas	Pancrea
6	chr7:2890400-2896400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:2891600-2902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:2891600-2902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:2891600-2902600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr7:2891600-2902800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr7:2892800-2902000	Weak transcription	NHLF	lung
12	chr7:2893200-2895800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr7:2893200-2902000	Weak transcription	Ovary	ovary
14	chr7:2893400-2900200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:2893400-2902600	Weak transcription	GM12878-XiMat	blood

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