Variant report

Variant	rs278379
Chromosome Location	chr3:98529164-98529165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10935513	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10935514	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1095911	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12632798	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12695786	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13081543	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13316760	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13319666	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1371687	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2062059	0.84[CHB][hapmap]
rs2333923	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2439237	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs278376	0.92[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes]
rs278380	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278381	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278382	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278387	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278388	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278390	0.88[CEU][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35760367	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4546099	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4857415	0.81[EUR][1000 genomes]
rs6767370	0.81[EUR][1000 genomes]
rs6774875	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6791389	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7615628	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7615856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs828603	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs828605	0.92[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs828610	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs828614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828616	0.88[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs828617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs828621	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]
rs852701	0.92[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8833	0.88[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs955351	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9682876	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837206	0.85[EUR][1000 genomes]
rs9842522	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880179	0.85[EUR][1000 genomes];0.84[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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs278379	DCBLD2	cis	Skin Sun Exposed Lower leg	GTEx
rs278379	ZBTB11	cis	cerebellum	SCAN
rs278379	ST3GAL6	cis	multi-tissue	Pritchard
rs278379	DCBLD2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:98503400-98576400	Weak transcription	Gastric	stomach
3	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
4	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
6	chr3:98515600-98533400	Weak transcription	Fetal Intestine Small	intestine
7	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
8	chr3:98517200-98531400	Weak transcription	Hela-S3	cervix
9	chr3:98522400-98533800	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr3:98523400-98531400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:98523600-98533800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:98523600-98535200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:98523800-98529200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:98523800-98529200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:98523800-98529200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr3:98523800-98529400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:98523800-98529400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:98523800-98529600	Strong transcription	Fetal Lung	lung
19	chr3:98523800-98530000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:98523800-98530200	Strong transcription	Dnd41	blood
21	chr3:98523800-98530400	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr3:98523800-98530400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:98523800-98530600	Strong transcription	HUVEC	blood vessel
24	chr3:98523800-98531400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:98523800-98531400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:98523800-98533600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:98523800-98533600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:98523800-98533800	Strong transcription	NHDF-Ad	bronchial
29	chr3:98523800-98535000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:98524200-98530400	Strong transcription	NHLF	lung
33	chr3:98524200-98544200	Strong transcription	HSMM	muscle
34	chr3:98524800-98530400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:98525400-98529200	Genic enhancers	NH-A	brain
36	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
37	chr3:98526200-98543200	Weak transcription	Lung	lung
38	chr3:98526400-98529200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:98526400-98532000	Weak transcription	Esophagus	oesophagus
40	chr3:98526400-98533600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:98526400-98535600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:98526400-98536000	Weak transcription	Aorta	Aorta
43	chr3:98526400-98538200	Weak transcription	GM12878-XiMat	blood
44	chr3:98526400-98539200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:98526400-98539400	Weak transcription	Fetal Brain Male	brain
46	chr3:98526400-98542800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:98526400-98544200	Weak transcription	Brain Angular Gyrus	brain
48	chr3:98526400-98545000	Weak transcription	Psoas Muscle	Psoas
49	chr3:98526600-98533800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:98526600-98537400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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