Variant report

Variant	rs220761
Chromosome Location	chr6:165823608-165823609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs17193	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs220749	0.88[ASN][1000 genomes]
rs220759	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs220762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220763	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220764	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs220766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs220767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220768	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220769	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs220770	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs220772	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs220774	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs220775	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs220776	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs220777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs220778	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs220780	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs220781	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs220784	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs220788	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs220789	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs220790	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs220793	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220797	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs220798	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs220799	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs220803	0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs220804	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs220805	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs545605	0.86[ASN][1000 genomes]
rs545609	0.86[ASN][1000 genomes]
rs578592	0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

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
rs220761	SMOC2	cis	parietal	SCAN
rs220761	PDE10A	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr6:165802000-165827200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:165802800-165831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:165804200-165828200	Weak transcription	Hela-S3	cervix
9	chr6:165804200-165831400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:165804400-165826000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:165804400-165827600	Weak transcription	HSMMtube	muscle
12	chr6:165806400-165826000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:165806400-165862000	Weak transcription	Right Ventricle	heart
14	chr6:165808800-165824200	Weak transcription	Left Ventricle	heart
15	chr6:165813600-165826400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:165813800-165831600	Weak transcription	Brain Germinal Matrix	brain
17	chr6:165814200-165853800	Weak transcription	Fetal Lung	lung
18	chr6:165816800-165850600	Weak transcription	Aorta	Aorta
19	chr6:165817000-165835800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:165818000-165824000	Weak transcription	HSMM	muscle
21	chr6:165818400-165835800	Weak transcription	Fetal Brain Male	brain
22	chr6:165818400-165848000	Weak transcription	Spleen	Spleen
23	chr6:165818800-165829600	Weak transcription	Gastric	stomach
24	chr6:165818800-165847200	Weak transcription	Fetal Heart	heart
25	chr6:165819000-165831400	Weak transcription	Fetal Brain Female	brain
26	chr6:165822800-165833800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:165823000-165833600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:165823200-165824000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:165823200-165834400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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