Variant report

Variant	rs6562915
Chromosome Location	chr13:76170886-76170887
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12427755	0.92[ASN][1000 genomes]
rs12427931	0.92[ASN][1000 genomes]
rs12428989	0.92[ASN][1000 genomes]
rs1535724	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2031236	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs2296146	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs2328959	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2328960	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2328963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328964	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2876706	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3783028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818355	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4611344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4643195	0.85[CHD][hapmap]
rs4885308	0.81[CHB][hapmap]
rs4885318	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4885322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885324	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55777620	0.99[ASN][1000 genomes]
rs55927305	0.93[ASN][1000 genomes]
rs6562912	0.92[JPT][hapmap];0.96[YRI][hapmap]
rs6562913	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6562914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6562916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6562918	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139740	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7317250	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223968	0.96[ASN][1000 genomes]
rs73223984	1.00[ASN][1000 genomes]
rs7324195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7329512	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7339146	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7981698	0.92[ASN][1000 genomes]
rs7982517	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7986566	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7989568	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7996884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8192755	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8192756	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8192762	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8192763	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8192764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9318361	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530447	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9543957	0.81[CHB][hapmap]
rs9543972	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9543976	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.96[ASN][1000 genomes]
rs9543990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9543992	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9544004	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9565177	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9573577	0.81[CHB][hapmap]
rs9573578	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs9573591	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9573592	0.95[ASN][1000 genomes]
rs974373	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900562	chr13:76072743-76176680	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv900570	chr13:76123678-76176680	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv900571	chr13:76123678-76207565	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv900576	chr13:76132484-76176680	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv900577	chr13:76132484-76207565	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	esv2751152	chr13:76144199-76288418	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6562915	COMMD6	cis	cerebellum	SCAN
rs6562915	UCHL3	cis	cerebellum	SCAN
rs6562915	UCHL3	cis	parietal	SCAN
rs6562915	RP11-173B14.5	cis	Artery Tibial	GTEx
rs6562915	SLAIN1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76124600-76183000	Weak transcription	Small Intestine	intestine
2	chr13:76125000-76192800	Weak transcription	Brain Substantia Nigra	brain
3	chr13:76125000-76209600	Weak transcription	Right Ventricle	heart
4	chr13:76125200-76173800	Weak transcription	Fetal Heart	heart
5	chr13:76125200-76177800	Weak transcription	Stomach Mucosa	stomach
6	chr13:76125400-76191000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr13:76125600-76182000	Weak transcription	Fetal Brain Male	brain
8	chr13:76129400-76180400	Weak transcription	Thymus	Thymus
9	chr13:76141800-76178400	Weak transcription	HepG2	liver
10	chr13:76144000-76192400	Weak transcription	NHLF	lung
11	chr13:76144200-76194400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr13:76144400-76176800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr13:76148000-76173800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:76148000-76174200	Weak transcription	HSMMtube	muscle
15	chr13:76148000-76178600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr13:76148200-76177200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr13:76148200-76192200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr13:76148200-76203000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:76148200-76209600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr13:76149000-76179000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr13:76149800-76172200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr13:76149800-76174200	Weak transcription	Psoas Muscle	Psoas
23	chr13:76149800-76180200	Weak transcription	NH-A	brain
24	chr13:76149800-76209600	Weak transcription	Lung	lung
25	chr13:76156800-76174000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr13:76158400-76192200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:76158600-76177200	Weak transcription	Left Ventricle	heart
28	chr13:76158600-76182400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr13:76158600-76191400	Weak transcription	Fetal Intestine Small	intestine
30	chr13:76158600-76195200	Weak transcription	NHEK	skin
31	chr13:76158800-76182000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr13:76159000-76194600	Weak transcription	HUVEC	blood vessel
33	chr13:76159000-76209600	Weak transcription	Brain Hippocampus Middle	brain
34	chr13:76159200-76173600	Weak transcription	NHDF-Ad	bronchial
35	chr13:76159200-76178200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr13:76159200-76180400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr13:76159200-76182600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr13:76159200-76186800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr13:76159200-76191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr13:76159400-76173400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr13:76159400-76174800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr13:76159400-76189800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr13:76159400-76201800	Weak transcription	Fetal Lung	lung
44	chr13:76160000-76180400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr13:76160200-76184600	Weak transcription	Fetal Kidney	kidney
46	chr13:76162600-76183400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr13:76164200-76181200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr13:76164400-76179000	Weak transcription	Pancreas	Pancrea
49	chr13:76164400-76183000	Weak transcription	Hela-S3	cervix
50	chr13:76164600-76171000	Weak transcription	Rectal Mucosa Donor 29	rectum

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