Variant report

Variant	rs1280044
Chromosome Location	chr6:76522602-76522603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1280039	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1280047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280048	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1321161	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1321162	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs2038624	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2038625	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2133190	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs2647417	0.83[ASN][1000 genomes]
rs2748943	0.83[ASN][1000 genomes]
rs2748944	0.81[ASN][1000 genomes]
rs2748946	0.83[ASN][1000 genomes]
rs2748947	0.83[ASN][1000 genomes]
rs2748954	0.83[ASN][1000 genomes]
rs2748955	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2748956	0.80[CEU][hapmap]
rs276685	0.80[MEX][hapmap]
rs276697	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs276698	0.83[ASW][hapmap];0.93[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs276699	0.81[CHB][hapmap]
rs2842553	0.85[ASN][1000 genomes]
rs2842556	0.81[CEU][hapmap]
rs2842558	0.83[ASN][1000 genomes]
rs2842559	0.81[ASN][1000 genomes]
rs3778006	0.86[CHB][hapmap]
rs3798439	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3822957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3857468	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6453845	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6903077	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6905047	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6906615	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6920348	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6938349	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6942367	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs721264	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9343316	0.82[MEX][hapmap]
rs9359139	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9360940	0.81[AMR][1000 genomes]
rs9443189	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9447539	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022428	chr6:76023118-76575620	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv538312	chr6:76023118-76575620	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
3	nsv1032245	chr6:76045537-76545703	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv538313	chr6:76045537-76545703	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv1017542	chr6:76238459-76537447	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
9	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv1032961	chr6:76343575-76788852	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1028340	chr6:76410921-76960225	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv538319	chr6:76410921-76960225	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1280044	SENP6	Cis_1M	lymphoblastoid	RTeQTL
rs1280044	DDX43	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76472600-76528000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:76485400-76523000	Weak transcription	Lung	lung
3	chr6:76491200-76523000	Weak transcription	Fetal Intestine Large	intestine
4	chr6:76492400-76523000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:76501800-76540800	Weak transcription	Left Ventricle	heart
6	chr6:76502600-76527400	Weak transcription	HUVEC	blood vessel
7	chr6:76505200-76527200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:76505600-76523000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:76506000-76523200	Weak transcription	Brain Anterior Caudate	brain
10	chr6:76507200-76523000	Weak transcription	Fetal Stomach	stomach
11	chr6:76509600-76528000	Weak transcription	NH-A	brain
12	chr6:76512000-76522800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:76512000-76528000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:76512400-76522800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:76513800-76523000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:76514200-76523000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:76516800-76523000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:76519400-76542600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:76520200-76576400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:76520600-76540600	Weak transcription	Aorta	Aorta
21	chr6:76521200-76523000	Weak transcription	Brain Substantia Nigra	brain
22	chr6:76521200-76542600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:76521200-76542800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:76521400-76523000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:76521400-76527800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:76521400-76546200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:76521400-76547600	Weak transcription	Colonic Mucosa	Colon
28	chr6:76521600-76523200	Weak transcription	Brain Angular Gyrus	brain
29	chr6:76521800-76527600	Weak transcription	Liver	Liver
30	chr6:76521800-76527800	Weak transcription	Adipose Nuclei	Adipose
31	chr6:76521800-76571000	Weak transcription	Gastric	stomach
32	chr6:76522000-76523200	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:76522000-76527400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:76522000-76558800	Weak transcription	Ovary	ovary
35	chr6:76522200-76542600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:76522200-76554200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:76522400-76523800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:76522400-76525200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:76522600-76523000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:76522600-76523400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr6:76522600-76524400	Strong transcription	Fetal Intestine Small	intestine
42	chr6:76522600-76559000	Weak transcription	Fetal Kidney	kidney

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