Variant report

Variant	rs16897785
Chromosome Location	chr6:165799958-165799959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11967995	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11969826	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1511746	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16897788	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16897792	1.00[CEU][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs220803	0.80[YRI][hapmap]
rs483260	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs488341	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs491517	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs491522	0.81[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs514500	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs515698	0.82[EUR][1000 genomes]
rs519368	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs531995	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs538464	0.80[MEX][hapmap]
rs541254	0.95[GIH][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes]
rs546496	0.81[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55847225	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs573291	0.81[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs576177	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58467288	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58724322	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58878073	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59352376	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59400673	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61366702	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61430416	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62442153	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66848668	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67480658	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs693799	0.81[EUR][1000 genomes]
rs705782	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs827489	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv2762630	chr6:165798068-165806114	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16897785	SMOC2	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:165744800-165801200	Weak transcription	Hela-S3	cervix
2	chr6:165745600-165802800	Weak transcription	Fetal Heart	heart
3	chr6:165747400-165802600	Weak transcription	HSMMtube	muscle
4	chr6:165747600-165853000	Weak transcription	A549	lung
5	chr6:165764400-165813400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:165772000-165835800	Weak transcription	Fetal Kidney	kidney
7	chr6:165779800-165805000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:165787400-165813400	Weak transcription	Fetal Lung	lung
9	chr6:165788000-165856800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:165788400-165803600	Weak transcription	Fetal Stomach	stomach
11	chr6:165790000-165810600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:165790200-165831400	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:165790400-165804000	Weak transcription	Aorta	Aorta
14	chr6:165790400-165811400	Weak transcription	Ovary	ovary
15	chr6:165791400-165834000	Weak transcription	Brain Anterior Caudate	brain
16	chr6:165794000-165807400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:165795200-165801000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:165795800-165804000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:165796000-165813400	Weak transcription	Brain Germinal Matrix	brain
20	chr6:165796400-165823000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:165796800-165806400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:165797200-165807600	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:165797400-165800600	Weak transcription	Right Ventricle	heart
24	chr6:165797800-165809800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:165798000-165803600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:165798000-165804400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:165798200-165804400	Strong transcription	Left Ventricle	heart
28	chr6:165798400-165802600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:165798800-165802000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:165798800-165804400	Strong transcription	Fetal Brain Female	brain
31	chr6:165799000-165817600	Weak transcription	Fetal Brain Male	brain
32	chr6:165799200-165801600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:165799200-165805800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:165799200-165808600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:165799200-165811800	Weak transcription	Brain Angular Gyrus	brain
36	chr6:165799600-165800400	Weak transcription	HSMM	muscle

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