Variant report

Variant	rs2299878
Chromosome Location	chr6:119578876-119578877
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119577142..119579813-chr6:119669541..119672184,2	K562	blood:
2	chr6:119578497..119580438-chr6:119630996..119632847,2	K562	blood:

Variant related genes	Relation type
ENSG00000111885	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12209570	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12215906	0.94[ASN][1000 genomes]
rs1295391	0.86[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs1295392	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs1324554	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs195048	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs195056	0.88[EUR][1000 genomes]
rs195058	0.90[EUR][1000 genomes]
rs195090	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs195092	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2057554	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2267673	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2267674	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2267675	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2267676	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299886	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2357164	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778111	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs3819731	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946406	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6937640	0.83[EUR][1000 genomes]
rs7755155	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7755572	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9489630	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9489633	0.83[AFR][1000 genomes]
rs9489638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs975578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119547400-119583000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:119558800-119582200	Weak transcription	Colonic Mucosa	Colon
3	chr6:119558800-119589800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:119558800-119590200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:119558800-119590400	Weak transcription	GM12878-XiMat	blood
6	chr6:119558800-119602000	Weak transcription	Gastric	stomach
7	chr6:119562200-119579400	Weak transcription	NHEK	skin
8	chr6:119562600-119580000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:119562600-119580000	Weak transcription	Small Intestine	intestine
10	chr6:119562800-119582200	Weak transcription	Pancreas	Pancrea
11	chr6:119562800-119583000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:119562800-119590200	Weak transcription	Fetal Stomach	stomach
13	chr6:119562800-119590800	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:119563400-119588000	Weak transcription	Fetal Kidney	kidney
15	chr6:119563400-119590200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:119566800-119582600	Weak transcription	Fetal Lung	lung
17	chr6:119568600-119592600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr6:119569000-119581600	Weak transcription	NHDF-Ad	bronchial
19	chr6:119569000-119583000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:119569200-119589800	Weak transcription	Fetal Intestine Large	intestine
21	chr6:119569200-119590000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:119569200-119590400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:119569200-119591600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:119569200-119591600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:119569400-119581400	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:119569400-119590000	Weak transcription	Placenta	Placenta
27	chr6:119569400-119590200	Weak transcription	Left Ventricle	heart
28	chr6:119569400-119591600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:119569800-119582600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:119570000-119580000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:119571000-119581400	Weak transcription	Adipose Nuclei	Adipose
32	chr6:119571600-119583800	Weak transcription	Primary B cells from cord blood	blood
33	chr6:119573000-119580000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:119574200-119583800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:119574200-119589800	Weak transcription	Fetal Intestine Small	intestine
36	chr6:119574800-119581400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:119576800-119580200	Weak transcription	Liver	Liver
38	chr6:119577000-119583800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:119577000-119583800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:119577000-119588800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr6:119577800-119579000	Genic enhancers	HepG2	liver
42	chr6:119577800-119580200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:119578200-119579400	Enhancers	Dnd41	blood
44	chr6:119578200-119579400	Flanking Active TSS	K562	blood
45	chr6:119578400-119579000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:119578600-119579600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:119578600-119580400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:119578600-119588800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:119578800-119579000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:119578800-119580000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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