Variant report

Variant	rs2561403
Chromosome Location	chr6:39194363-39194364
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	chr6:39170012..39173010-chr6:39194285..39196889,3	MCF-7	breast:
2	chr6:39192543..39195270-chr6:39259985..39261560,2	K562	blood:
3	chr6:39193484..39195491-chr6:39238843..39241224,2	K562	blood:
4	chr6:39171917..39173795-chr6:39193843..39195805,2	MCF-7	breast:
5	chr6:39145278..39148548-chr6:39191713..39196059,4	K562	blood:
6	chr6:39148774..39151359-chr6:39193575..39195195,2	K562	blood:
7	chr6:39156367..39160126-chr6:39192413..39195568,3	K562	blood:
8	chr6:39194146..39197134-chr6:39221848..39224587,2	K562	blood:

No data

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2561402	1.00[JPT][hapmap]
rs2561404	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2815125	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9471013	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3352542	chr6:39194298-39194661	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39174200-39195000	Enhancers	Stomach Mucosa	stomach
2	chr6:39182200-39195200	Enhancers	Fetal Lung	lung
3	chr6:39185000-39194400	Enhancers	Ovary	ovary
4	chr6:39186200-39195000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:39188800-39195000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:39189600-39194600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:39189800-39195400	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr6:39190000-39195600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:39191000-39195000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr6:39191400-39196000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:39191800-39194400	Weak transcription	Fetal Kidney	kidney
12	chr6:39191800-39194800	Enhancers	H9 Cell Line	embryonic stem cell
13	chr6:39192000-39195600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:39192200-39195000	Enhancers	Placenta	Placenta
15	chr6:39192200-39195200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:39192200-39196000	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:39192400-39195200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:39192400-39195400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr6:39192600-39194600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr6:39192600-39195000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:39192800-39195000	Enhancers	Colonic Mucosa	Colon
22	chr6:39192800-39195000	Active TSS	Rectal Smooth Muscle	rectum
23	chr6:39193000-39195400	Enhancers	Primary B cells from cord blood	blood
24	chr6:39193000-39195600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:39193200-39194400	Weak transcription	Fetal Stomach	stomach
26	chr6:39193200-39194400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr6:39193200-39194600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr6:39193200-39194600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr6:39193200-39195400	Enhancers	Primary T cells from cord blood	blood
30	chr6:39193200-39195600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:39193200-39195800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr6:39193200-39196000	Enhancers	Thymus	Thymus
33	chr6:39193200-39196600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:39193400-39194400	Enhancers	Hela-S3	cervix
35	chr6:39193400-39194600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr6:39193400-39194800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr6:39193400-39194800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:39193600-39194400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr6:39193600-39194400	Enhancers	A549	lung
40	chr6:39193600-39194600	Flanking Active TSS	Liver	Liver
41	chr6:39193600-39195000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr6:39193600-39195200	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr6:39193600-39196200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr6:39193800-39194400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
45	chr6:39193800-39194600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:39193800-39194600	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr6:39193800-39194600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr6:39193800-39194800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:39193800-39194800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr6:39193800-39194800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links