Variant report

Variant	rs3798485
Chromosome Location	chr6:100906504-100906505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12663321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12663539	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17054156	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17060650	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17060652	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs241814	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3756915	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56681764	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73496769	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73496776	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73496787	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7746426	0.91[AMR][1000 genomes];0.90[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	chr6:100905400-100906800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:100905400-100906800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:100905400-100906800	ZNF genes & repeats	Lung	lung
13	chr6:100905600-100906600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:100905600-100906600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:100905600-100906600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr6:100905600-100906800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:100905800-100906600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:100905800-100906800	Bivalent Enhancer	Fetal Stomach	stomach
19	chr6:100906000-100906600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:100906000-100906600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:100906000-100906600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:100906000-100906600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
23	chr6:100906000-100906600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr6:100906000-100906600	Bivalent Enhancer	Esophagus	oesophagus
25	chr6:100906000-100906600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
26	chr6:100906000-100906600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
27	chr6:100906000-100906600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr6:100906000-100906800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:100906000-100906800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr6:100906000-100906800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:100906000-100906800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:100906000-100906800	Flanking Active TSS	Pancreas	Pancrea
33	chr6:100906200-100906600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
34	chr6:100906200-100906600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
35	chr6:100906200-100906600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
36	chr6:100906200-100906600	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:100906200-100906600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
38	chr6:100906200-100906600	Flanking Active TSS	Right Ventricle	heart
39	chr6:100906200-100906600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
40	chr6:100906200-100906600	Bivalent Enhancer	HMEC	breast
41	chr6:100906200-100906800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
42	chr6:100906200-100907000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:100906400-100906600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
44	chr6:100906400-100906600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:100906400-100906600	Bivalent Enhancer	Adipose Nuclei	Adipose
46	chr6:100906400-100906600	Bivalent Enhancer	Colonic Mucosa	Colon
47	chr6:100906400-100906600	Flanking Bivalent TSS/Enh	Gastric	stomach
48	chr6:100906400-100906800	Bivalent Enhancer	HUVEC	blood vessel
49	chr6:100906400-100907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:100906400-100908400	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links