Variant report

Variant	rs580507
Chromosome Location	chr2:169718902-169718903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:169710784..169714021-chr2:169716907..169719872,4	K562	blood:

Variant related genes	Relation type
ENSG00000163072	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2461385	0.82[EUR][1000 genomes]
rs2685800	1.00[EUR][1000 genomes]
rs2685801	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs475467	0.95[EUR][1000 genomes]
rs477309	0.94[EUR][1000 genomes]
rs479661	0.98[EUR][1000 genomes]
rs494859	0.95[EUR][1000 genomes]
rs498041	0.96[EUR][1000 genomes]
rs499160	0.96[EUR][1000 genomes]
rs504393	0.96[EUR][1000 genomes]
rs509988	0.94[EUR][1000 genomes]
rs511778	0.96[EUR][1000 genomes]
rs525428	0.96[EUR][1000 genomes]
rs533492	1.00[EUR][1000 genomes]
rs534771	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs539400	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs560494	0.92[EUR][1000 genomes]
rs576338	0.96[EUR][1000 genomes]
rs577192	1.00[EUR][1000 genomes]
rs581363	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs830021	0.82[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	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv875381	chr2:169686559-169749841	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv516627	chr2:169714893-169721377	Strong transcription Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs580507	DYNC1I2	cis	cerebellum	SCAN
rs580507	COBLL1	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169689000-169721800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:169693400-169721400	Weak transcription	Spleen	Spleen
3	chr2:169693600-169721400	Weak transcription	Right Ventricle	heart
4	chr2:169698400-169721200	Weak transcription	Stomach Mucosa	stomach
5	chr2:169698600-169744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:169702200-169721200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:169702200-169733000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:169702600-169721400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:169703600-169721200	Weak transcription	GM12878-XiMat	blood
10	chr2:169704200-169723400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:169704600-169721400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:169705000-169721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:169705000-169723600	Weak transcription	Fetal Brain Female	brain
14	chr2:169705200-169721400	Weak transcription	Fetal Kidney	kidney
15	chr2:169706000-169719000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:169706600-169721600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:169706600-169727800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:169707000-169721000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:169707400-169722000	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr2:169708600-169723200	Weak transcription	NHLF	lung
21	chr2:169708800-169721000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:169708800-169721200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:169708800-169721200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:169708800-169721200	Weak transcription	A549	lung
25	chr2:169708800-169721200	Weak transcription	HMEC	breast
26	chr2:169709200-169721400	Weak transcription	HUVEC	blood vessel
27	chr2:169709400-169721000	Weak transcription	Colonic Mucosa	Colon
28	chr2:169709400-169721200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:169709800-169721000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:169709800-169733400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:169710000-169719000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:169710200-169721200	Weak transcription	Fetal Lung	lung
33	chr2:169710200-169721400	Weak transcription	NHEK	skin
34	chr2:169710400-169721200	Strong transcription	K562	blood
35	chr2:169711400-169721000	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:169711400-169721600	Weak transcription	NH-A	brain
37	chr2:169712600-169721200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:169712600-169727800	Weak transcription	Primary T cells from cord blood	blood
39	chr2:169713200-169720600	Weak transcription	Hela-S3	cervix
40	chr2:169713200-169721200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:169713200-169728800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:169713400-169720000	Weak transcription	Psoas Muscle	Psoas
43	chr2:169713400-169721200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:169713400-169721200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:169713400-169722000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr2:169713400-169731200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:169713600-169722000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:169713800-169719000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:169713800-169721200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:169714000-169719600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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