Variant report

Variant	rs2576707
Chromosome Location	chr2:55551931-55551932
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	chr2:55543117..55545665-chr2:55550405..55552133,2	K562	blood:
2	chr2:55550452..55552052-chr2:55563952..55565660,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10189439	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11125567	0.81[ASN][1000 genomes]
rs11680143	0.85[ASN][1000 genomes]
rs11692239	0.83[ASN][1000 genomes]
rs12470528	0.84[ASN][1000 genomes]
rs12476508	0.85[ASN][1000 genomes]
rs12476548	0.85[ASN][1000 genomes]
rs12713292	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1344881	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1437394	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1545555	0.85[ASN][1000 genomes]
rs1902059	0.81[ASN][1000 genomes]
rs1982484	0.85[ASN][1000 genomes]
rs1982485	0.83[ASN][1000 genomes]
rs1992127	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992128	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576687	0.91[ASN][1000 genomes]
rs2576704	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576705	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576706	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2576713	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2576714	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2576715	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2576716	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576717	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589055	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589056	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589059	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589065	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589066	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2589072	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2589073	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2589075	0.91[ASN][1000 genomes]
rs2589084	0.83[ASN][1000 genomes]
rs2589085	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2589087	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2589088	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2589090	0.91[ASN][1000 genomes]
rs2589091	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2589102	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2589103	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2589105	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2589106	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2864828	0.91[ASN][1000 genomes]
rs2864829	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2864830	0.91[ASN][1000 genomes]
rs2867180	0.82[ASN][1000 genomes]
rs2867181	0.85[ASN][1000 genomes]
rs2903508	0.82[ASN][1000 genomes]
rs2917776	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2917778	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2920964	0.84[ASN][1000 genomes]
rs2920971	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920974	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2966467	0.91[ASN][1000 genomes]
rs3099075	0.90[ASN][1000 genomes]
rs3099076	0.91[ASN][1000 genomes]
rs3099077	0.91[ASN][1000 genomes]
rs3099079	0.91[ASN][1000 genomes]
rs3099082	0.91[ASN][1000 genomes]
rs3099084	0.91[ASN][1000 genomes]
rs3111404	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3111410	0.92[ASN][1000 genomes]
rs3111411	0.92[ASN][1000 genomes]
rs3111412	0.91[ASN][1000 genomes]
rs3111413	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs35963448	0.88[ASN][1000 genomes]
rs3762510	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3791633	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3791634	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3791653	0.92[ASN][1000 genomes]
rs4349381	0.88[ASN][1000 genomes]
rs55711116	0.83[ASN][1000 genomes]
rs55908714	0.83[ASN][1000 genomes]
rs57410428	0.87[ASN][1000 genomes]
rs62137151	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137154	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62137157	0.83[ASN][1000 genomes]
rs6545487	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6545488	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6706178	0.81[ASN][1000 genomes]
rs6725124	0.81[ASN][1000 genomes]
rs6727038	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7564292	0.90[ASN][1000 genomes]
rs7570934	0.83[ASN][1000 genomes]
rs7575929	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7576695	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7582580	0.91[ASN][1000 genomes]
rs7586529	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2576707	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
4	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
5	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
6	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
8	chr2:55520200-55554400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
12	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
15	chr2:55537800-55554600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:55537800-55609400	Weak transcription	Lung	lung
17	chr2:55538600-55557000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:55539200-55567800	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:55539200-55579000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:55539200-55579000	Weak transcription	NHEK	skin
21	chr2:55539400-55553000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:55539400-55553600	Weak transcription	NHLF	lung
23	chr2:55539800-55554400	Weak transcription	Fetal Heart	heart
24	chr2:55541400-55554200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:55541400-55564600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:55541400-55584400	Weak transcription	Spleen	Spleen
27	chr2:55541600-55553000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:55541600-55557600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:55541800-55574800	Weak transcription	Ovary	ovary
30	chr2:55542400-55559800	Weak transcription	Fetal Brain Male	brain
31	chr2:55542400-55560400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:55542400-55589800	Weak transcription	Fetal Intestine Large	intestine
33	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
34	chr2:55542600-55554200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:55542600-55563000	Weak transcription	Thymus	Thymus
36	chr2:55542800-55552600	Weak transcription	A549	lung
37	chr2:55542800-55554000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:55542800-55557000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:55543000-55554400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:55543000-55555800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:55543200-55552200	Weak transcription	HMEC	breast
42	chr2:55543200-55554000	Weak transcription	HSMMtube	muscle
43	chr2:55543600-55552800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:55543800-55554400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:55544200-55581800	Weak transcription	Left Ventricle	heart
46	chr2:55545200-55553200	Weak transcription	Fetal Kidney	kidney
47	chr2:55546000-55554200	Weak transcription	Placenta	Placenta
48	chr2:55546000-55557000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:55546200-55552000	Weak transcription	Fetal Lung	lung
50	chr2:55546200-55552600	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links