Variant report

Variant	rs3799568
Chromosome Location	chr6:167035835-167035836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167035604..167038235-chr6:167040017..167042758,3	K562	blood:

Variant related genes	Relation type
ENSG00000071242	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1106933	0.85[CEU][hapmap]
rs16899289	0.80[AMR][1000 genomes]
rs2206124	0.80[AMR][1000 genomes]
rs2223407	0.80[AMR][1000 genomes]
rs4145432	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58803664	0.80[AMR][1000 genomes]
rs61157638	0.80[AMR][1000 genomes]
rs62438673	0.80[AMR][1000 genomes]
rs873069	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs9348157	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9348159	0.80[AMR][1000 genomes]
rs9348160	0.80[AMR][1000 genomes]
rs9356499	0.80[AMR][1000 genomes]
rs9364863	0.80[AMR][1000 genomes]
rs9366036	0.84[AMR][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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv432984	chr6:167018915-167181613	Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1023649	chr6:167026469-167060732	Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3799568	DLL1	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167029200-167039000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:167029400-167036800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:167031600-167037200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr6:167032600-167038600	Enhancers	NHLF	lung
5	chr6:167032600-167039400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:167032800-167036600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:167032800-167039000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:167032800-167039000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:167033200-167039000	Enhancers	HUVEC	blood vessel
10	chr6:167033600-167036800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:167033600-167039000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:167034400-167036000	Enhancers	NHEK	skin
13	chr6:167034400-167036000	Enhancers	Osteobl	bone
14	chr6:167034400-167039000	Weak transcription	Liver	Liver
15	chr6:167034600-167036400	Weak transcription	Right Ventricle	heart
16	chr6:167034600-167036800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:167034600-167036800	Weak transcription	Esophagus	oesophagus
18	chr6:167034600-167037800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:167034600-167037800	Weak transcription	Brain Substantia Nigra	brain
20	chr6:167034600-167037800	Weak transcription	Fetal Lung	lung
21	chr6:167034600-167038800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:167034600-167038800	Enhancers	HMEC	breast
23	chr6:167034600-167038800	Weak transcription	HSMMtube	muscle
24	chr6:167034600-167039000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:167034800-167036200	Enhancers	NH-A	brain
26	chr6:167034800-167036400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:167034800-167036600	Genic enhancers	Muscle Satellite Cultured Cells	--
28	chr6:167034800-167036800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:167034800-167036800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:167034800-167036800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:167034800-167036800	Weak transcription	Aorta	Aorta
32	chr6:167034800-167036800	Weak transcription	Gastric	stomach
33	chr6:167034800-167036800	Weak transcription	Ovary	ovary
34	chr6:167034800-167036800	Weak transcription	Psoas Muscle	Psoas
35	chr6:167034800-167036800	Weak transcription	Right Atrium	heart
36	chr6:167034800-167037000	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr6:167034800-167037000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:167034800-167037800	Weak transcription	Adipose Nuclei	Adipose
39	chr6:167034800-167037800	Weak transcription	Fetal Stomach	stomach
40	chr6:167034800-167037800	Weak transcription	HSMM	muscle
41	chr6:167034800-167038000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:167034800-167038800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:167034800-167038800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr6:167034800-167039000	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:167034800-167039000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:167034800-167039000	Weak transcription	Fetal Brain Male	brain
47	chr6:167034800-167039000	Weak transcription	Fetal Kidney	kidney
48	chr6:167034800-167039200	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:167034800-167039400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:167034800-167039800	Weak transcription	Spleen	Spleen

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