Variant report

Variant	rs2561402
Chromosome Location	chr6:39193638-39193639
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39192543..39195270-chr6:39259985..39261560,2	K562	blood:
2	chr6:39193484..39195491-chr6:39238843..39241224,2	K562	blood:
3	chr6:39145278..39148548-chr6:39191713..39196059,4	K562	blood:
4	chr6:39162719..39164812-chr6:39191321..39194021,2	K562	blood:
5	chr6:39148774..39151359-chr6:39193575..39195195,2	K562	blood:
6	chr6:39156367..39160126-chr6:39192413..39195568,3	K562	blood:
7	chr6:39152522..39154314-chr6:39191338..39193640,2	MCF-7	breast:
8	chr6:39186069..39188057-chr6:39192184..39193839,2	MCF-7	breast:

No data

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2561403	1.00[JPT][hapmap]
rs9462495	1.00[CEU][hapmap];0.91[ASN][1000 genomes]
rs9471013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9471016	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39150600-39193800	Genic enhancers	Fetal Intestine Small	intestine
2	chr6:39174200-39195000	Enhancers	Stomach Mucosa	stomach
3	chr6:39182200-39195200	Enhancers	Fetal Lung	lung
4	chr6:39185000-39194400	Enhancers	Ovary	ovary
5	chr6:39186000-39193800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:39186000-39193800	Genic enhancers	Fetal Intestine Large	intestine
7	chr6:39186200-39195000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:39188800-39195000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:39189400-39194200	Transcr. at gene 5' and 3'	K562	blood
10	chr6:39189600-39194600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:39189800-39195400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr6:39190000-39195600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:39190800-39194000	Enhancers	Small Intestine	intestine
14	chr6:39191000-39195000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr6:39191400-39196000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:39191600-39193800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:39191600-39193800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:39191600-39193800	Weak transcription	Esophagus	oesophagus
19	chr6:39191800-39194000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:39191800-39194400	Weak transcription	Fetal Kidney	kidney
21	chr6:39191800-39194800	Enhancers	H9 Cell Line	embryonic stem cell
22	chr6:39192000-39194200	Enhancers	Adipose Nuclei	Adipose
23	chr6:39192000-39195600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:39192200-39194000	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr6:39192200-39194200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:39192200-39195000	Enhancers	Placenta	Placenta
27	chr6:39192200-39195200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:39192200-39196000	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:39192400-39194000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:39192400-39194000	Enhancers	Spleen	Spleen
31	chr6:39192400-39195200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:39192400-39195400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr6:39192600-39194200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr6:39192600-39194600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr6:39192600-39195000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:39192800-39193800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:39192800-39193800	Genic enhancers	Fetal Thymus	thymus
38	chr6:39192800-39194200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:39192800-39195000	Enhancers	Colonic Mucosa	Colon
40	chr6:39192800-39195000	Active TSS	Rectal Smooth Muscle	rectum
41	chr6:39193000-39195400	Enhancers	Primary B cells from cord blood	blood
42	chr6:39193000-39195600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:39193200-39193800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:39193200-39194000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr6:39193200-39194000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:39193200-39194200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:39193200-39194400	Weak transcription	Fetal Stomach	stomach
48	chr6:39193200-39194400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr6:39193200-39194600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr6:39193200-39194600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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