Variant report

Variant	rs2328962
Chromosome Location	chr13:76175865-76175866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11840945	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12866456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12872149	0.95[ASN][1000 genomes]
rs1323696	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1535726	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2031235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274049	0.95[ASN][1000 genomes]
rs2281762	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2328961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3812844	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs3812845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3812846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4539477	0.81[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs4884008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885312	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885313	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4885314	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4885319	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4885321	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4885328	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4885330	0.94[ASN][1000 genomes]
rs4885331	0.94[ASN][1000 genomes]
rs4885332	0.94[ASN][1000 genomes]
rs4885333	0.94[ASN][1000 genomes]
rs4885334	0.92[ASN][1000 genomes]
rs61960594	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6562912	0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6562920	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7317893	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7319334	0.84[CHB][hapmap]
rs7319441	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7326807	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7331205	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7358977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7491365	0.91[ASN][1000 genomes]
rs7982534	0.86[ASN][1000 genomes]
rs7982613	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs7984443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7995040	0.84[CHB][hapmap]
rs7995889	0.83[ASN][1000 genomes]
rs8000062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[ASN][1000 genomes]
rs8192738	0.85[ASN][1000 genomes]
rs8192741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8192746	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs8192747	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8192748	0.81[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8192751	0.94[ASN][1000 genomes]
rs8192753	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs9318357	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9318358	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9530450	0.94[ASN][1000 genomes]
rs9530453	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9530456	0.92[ASN][1000 genomes]
rs9543969	0.81[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap]
rs9543980	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9543994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9543996	0.98[ASN][1000 genomes]
rs9543997	0.98[ASN][1000 genomes]
rs9543999	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9544008	0.95[ASN][1000 genomes]
rs9565175	0.94[ASN][1000 genomes]
rs9573580	0.81[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap]
rs9573584	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9573590	0.97[ASN][1000 genomes]
rs9635000	0.97[ASN][1000 genomes]
rs966058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs966059	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs972542	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs975938	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2328962	COMMD6	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

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	chr13:76125200-76177800	Weak transcription	Stomach Mucosa	stomach
5	chr13:76125400-76191000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr13:76125600-76182000	Weak transcription	Fetal Brain Male	brain
7	chr13:76129400-76180400	Weak transcription	Thymus	Thymus
8	chr13:76141800-76178400	Weak transcription	HepG2	liver
9	chr13:76144000-76192400	Weak transcription	NHLF	lung
10	chr13:76144200-76194400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr13:76144400-76176800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr13:76148000-76178600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr13:76148200-76177200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr13:76148200-76192200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:76148200-76203000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:76148200-76209600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr13:76149000-76179000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr13:76149800-76180200	Weak transcription	NH-A	brain
19	chr13:76149800-76209600	Weak transcription	Lung	lung
20	chr13:76158400-76192200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr13:76158600-76177200	Weak transcription	Left Ventricle	heart
22	chr13:76158600-76182400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:76158600-76191400	Weak transcription	Fetal Intestine Small	intestine
24	chr13:76158600-76195200	Weak transcription	NHEK	skin
25	chr13:76158800-76182000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr13:76159000-76194600	Weak transcription	HUVEC	blood vessel
27	chr13:76159000-76209600	Weak transcription	Brain Hippocampus Middle	brain
28	chr13:76159200-76178200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr13:76159200-76180400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr13:76159200-76182600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr13:76159200-76186800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr13:76159200-76191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr13:76159400-76189800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr13:76159400-76201800	Weak transcription	Fetal Lung	lung
35	chr13:76160000-76180400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr13:76160200-76184600	Weak transcription	Fetal Kidney	kidney
37	chr13:76162600-76183400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr13:76164200-76181200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:76164400-76179000	Weak transcription	Pancreas	Pancrea
40	chr13:76164400-76183000	Weak transcription	Hela-S3	cervix
41	chr13:76164600-76177200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr13:76164600-76177200	Weak transcription	Fetal Stomach	stomach
43	chr13:76164600-76178400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr13:76164600-76178800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr13:76164600-76179800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr13:76164600-76180600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr13:76164600-76181800	Weak transcription	Ovary	ovary
48	chr13:76164600-76182600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr13:76164600-76192000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:76164600-76194600	Weak transcription	Aorta	Aorta

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