Variant report

Variant	rs3778030
Chromosome Location	chr6:100906046-100906047
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1506080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17060614	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17060615	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1847912	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1857859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs241812	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs3213541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734353	0.84[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3778032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798488	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3798492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798495	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798497	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3830139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs767933	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7741057	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7757905	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390379	0.84[EUR][1000 genomes];0.85[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	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking 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
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats 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
5	nsv515895	chr6:100868779-100910798	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
6	nsv533053	chr6:100883636-100911512	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100897400-100908600	Weak transcription	HSMMtube	muscle
2	chr6:100901600-100906800	ZNF genes & repeats	Spleen	Spleen
3	chr6:100901600-100907200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:100901800-100907600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr6:100902000-100913600	Active TSS	Psoas Muscle	Psoas
6	chr6:100905200-100906600	Bivalent Enhancer	Liver	Liver
7	chr6:100905200-100906800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr6:100905200-100906800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:100905200-100906800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:100905400-100906200	Bivalent Enhancer	Right Ventricle	heart
11	chr6:100905400-100906200	Bivalent Enhancer	Stomach Mucosa	stomach
12	chr6:100905400-100906800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr6:100905400-100906800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr6:100905400-100906800	ZNF genes & repeats	Lung	lung
15	chr6:100905600-100906200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:100905600-100906400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
17	chr6:100905600-100906400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:100905600-100906400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:100905600-100906400	Bivalent Enhancer	Fetal Brain Male	brain
20	chr6:100905600-100906600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr6:100905600-100906600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:100905600-100906600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr6:100905600-100906800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:100905800-100906200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
25	chr6:100905800-100906200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr6:100905800-100906200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:100905800-100906200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr6:100905800-100906600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:100905800-100906800	Bivalent Enhancer	Fetal Stomach	stomach
30	chr6:100906000-100906200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:100906000-100906200	Bivalent Enhancer	Brain Germinal Matrix	brain
32	chr6:100906000-100906200	Bivalent Enhancer	Placenta	Placenta
33	chr6:100906000-100906200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr6:100906000-100906400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:100906000-100906400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr6:100906000-100906400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
37	chr6:100906000-100906600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:100906000-100906600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:100906000-100906600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:100906000-100906600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
41	chr6:100906000-100906600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr6:100906000-100906600	Bivalent Enhancer	Esophagus	oesophagus
43	chr6:100906000-100906600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
44	chr6:100906000-100906600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
45	chr6:100906000-100906600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr6:100906000-100906800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:100906000-100906800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
48	chr6:100906000-100906800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:100906000-100906800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:100906000-100906800	Flanking Active TSS	Pancreas	Pancrea

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