Variant report

Variant	rs28400886
Chromosome Location	chr6:29974675-29974676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF39-6	chr6:29973898-29974893	NONHSAT108579
2	lnc-ZNRD1-4	chr6:29974577-29974846	NR_024240

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12210298	1.00[ASN][1000 genomes]
rs9260673	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9260679	0.97[EUR][1000 genomes]
rs9260705	0.97[EUR][1000 genomes]
rs9260770	0.97[EUR][1000 genomes]
rs9260802	1.00[EUR][1000 genomes]
rs9260811	1.00[EUR][1000 genomes]
rs9260888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260924	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9260985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261267	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
8	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
12	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
13	nsv601475	chr6:29963179-29977973	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29973800-29974800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:29973800-29974800	Active TSS	Rectal Smooth Muscle	rectum
3	chr6:29973800-29974800	Bivalent/Poised TSS	Thymus	Thymus
4	chr6:29973800-29975000	Active TSS	Brain Anterior Caudate	brain
5	chr6:29973800-29975000	Flanking Bivalent TSS/Enh	Osteobl	bone
6	chr6:29973800-29975200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:29973800-29975200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:29973800-29975200	Active TSS	Aorta	Aorta
9	chr6:29973800-29975200	Bivalent/Poised TSS	NHDF-Ad	bronchial
10	chr6:29973800-29975200	Bivalent/Poised TSS	NHLF	lung
11	chr6:29973800-29975400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:29973800-29975400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:29973800-29975400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
14	chr6:29973800-29975400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:29973800-29975600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:29974000-29974800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:29974000-29974800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr6:29974000-29974800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
19	chr6:29974000-29974800	Active TSS	Brain Substantia Nigra	brain
20	chr6:29974000-29974800	Active TSS	Colon Smooth Muscle	Colon
21	chr6:29974000-29974800	Flanking Active TSS	Spleen	Spleen
22	chr6:29974000-29975000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
23	chr6:29974000-29975000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr6:29974000-29975000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
25	chr6:29974000-29975000	Flanking Bivalent TSS/Enh	Placenta	Placenta
26	chr6:29974000-29975000	Active TSS	Left Ventricle	heart
27	chr6:29974000-29975000	Active TSS	Psoas Muscle	Psoas
28	chr6:29974000-29975200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:29974000-29975200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
30	chr6:29974000-29975200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
31	chr6:29974000-29975200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:29974000-29975200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
33	chr6:29974000-29975200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
34	chr6:29974000-29975200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
35	chr6:29974000-29975200	Active TSS	Gastric	stomach
36	chr6:29974000-29975200	Flanking Active TSS	Ovary	ovary
37	chr6:29974000-29975200	Active TSS	Right Atrium	heart
38	chr6:29974000-29975200	Bivalent/Poised TSS	HSMM	muscle
39	chr6:29974000-29975400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr6:29974000-29975400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
41	chr6:29974000-29975400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:29974000-29975400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:29974000-29975400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:29974000-29975400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:29974000-29975400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:29974000-29975400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:29974000-29975400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:29974000-29975400	Flanking Active TSS	Liver	Liver
49	chr6:29974000-29975600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
50	chr6:29974000-29975600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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