Variant report

Variant	rs220748
Chromosome Location	chr6:165827643-165827644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1759948	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220739	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs220740	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs220741	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220742	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220743	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220744	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220745	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220746	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220747	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220765	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220773	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs220782	0.94[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs220783	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs220785	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs220786	0.97[ASN][1000 genomes]
rs220787	0.97[ASN][1000 genomes]
rs220791	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs220792	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs220794	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220795	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs220796	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs220813	0.81[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap]
rs572291	1.00[JPT][hapmap]

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	nsv432982	chr6:165528589-165835589	Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv605245	chr6:165542686-165845903	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv1031648	chr6:165544569-165841029	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv432983	chr6:165554403-165851585	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv3417270	chr6:165682773-166023032	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv886928	chr6:165722345-166197889	Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv830863	chr6:165803464-165970091	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv886929	chr6:165821402-165850480	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv886930	chr6:165823608-165850480	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs220748	VEGFC	trans	parietal	SCAN
rs220748	QKI	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:165747600-165853000	Weak transcription	A549	lung
2	chr6:165772000-165835800	Weak transcription	Fetal Kidney	kidney
3	chr6:165788000-165856800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:165790200-165831400	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:165791400-165834000	Weak transcription	Brain Anterior Caudate	brain
6	chr6:165802800-165831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:165804200-165828200	Weak transcription	Hela-S3	cervix
8	chr6:165804200-165831400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:165806400-165862000	Weak transcription	Right Ventricle	heart
10	chr6:165813800-165831600	Weak transcription	Brain Germinal Matrix	brain
11	chr6:165814200-165853800	Weak transcription	Fetal Lung	lung
12	chr6:165816800-165850600	Weak transcription	Aorta	Aorta
13	chr6:165817000-165835800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:165818400-165835800	Weak transcription	Fetal Brain Male	brain
15	chr6:165818400-165848000	Weak transcription	Spleen	Spleen
16	chr6:165818800-165829600	Weak transcription	Gastric	stomach
17	chr6:165818800-165847200	Weak transcription	Fetal Heart	heart
18	chr6:165819000-165831400	Weak transcription	Fetal Brain Female	brain
19	chr6:165822800-165833800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:165823000-165833600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:165823200-165834400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:165824600-165840400	Weak transcription	Ovary	ovary
23	chr6:165825600-165856200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:165825800-165829800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:165826000-165828400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:165826000-165829800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:165826000-165829800	Strong transcription	HSMM	muscle
28	chr6:165826600-165856000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:165827000-165828400	Strong transcription	Left Ventricle	heart
30	chr6:165827200-165828200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:165827400-165831600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr6:165827600-165828400	Strong transcription	HSMMtube	muscle

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