Variant report

Variant	rs2580770
Chromosome Location	chr2:55214912-55214913
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55212432-55217795	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55198988..55201900-chr2:55213351..55214997,2	MCF-7	breast:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12464877	1.00[ASW][hapmap]
rs13031431	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs17046514	1.00[ASW][hapmap]
rs17046579	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17046586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17046589	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1822617	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2255026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255393	0.85[CHB][hapmap]
rs2580768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2580769	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2580771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2588513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2588515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2588516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2588522	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2919126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2920859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972063	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34352825	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34378852	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34928331	0.96[ASN][1000 genomes]
rs35981204	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671993	1.00[ASW][hapmap]
rs4672003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4672018	1.00[ASW][hapmap]
rs6545464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6734314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739210	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72795434	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7355716	0.84[CHB][hapmap]

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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2580770	CCDC88A	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:55195000-55215200	Strong transcription	Dnd41	blood
3	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
5	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:55198600-55215200	Weak transcription	Lung	lung
9	chr2:55198800-55215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
11	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
12	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
13	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
14	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
15	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
16	chr2:55205800-55216000	Weak transcription	Fetal Intestine Small	intestine
17	chr2:55206600-55215200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:55207600-55215200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:55207800-55215200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:55208200-55216600	Weak transcription	Stomach Mucosa	stomach
21	chr2:55208400-55215000	Strong transcription	Primary B cells from cord blood	blood
22	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:55210800-55216000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:55211000-55218600	Weak transcription	Aorta	Aorta
25	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:55211600-55215400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:55211800-55215000	Strong transcription	Liver	Liver
28	chr2:55212000-55216000	Weak transcription	Fetal Heart	heart
29	chr2:55212200-55215000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:55212200-55215200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:55212200-55220600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:55212400-55215400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:55212600-55215000	Strong transcription	Hela-S3	cervix
34	chr2:55212600-55220200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:55212600-55226400	Weak transcription	Fetal Stomach	stomach
36	chr2:55212800-55215000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:55213000-55215000	Genic enhancers	Brain Cingulate Gyrus	brain
38	chr2:55213000-55215200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:55213000-55216000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:55213200-55215400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr2:55213200-55217200	Strong transcription	HSMM	muscle
42	chr2:55213400-55215000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:55213400-55215000	Strong transcription	Osteobl	bone
44	chr2:55213400-55217200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr2:55213600-55215200	Weak transcription	Psoas Muscle	Psoas
46	chr2:55213600-55215600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:55213800-55215000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:55213800-55215200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:55213800-55215200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:55213800-55217200	Enhancers	Brain Substantia Nigra	brain

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