Variant report

Variant	rs2010987
Chromosome Location	chr4:74472876-74472877
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	chr4:74472437..74474107-chr4:74481794..74484124,2	MCF-7	breast:
2	chr4:74469058..74470945-chr4:74472294..74475158,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11736697	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1247583	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs13131954	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13142786	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1534642	0.88[CEU][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17805665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2010989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446944	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1008104	chr4:74468434-74621952	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2010987	CNOT6L	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74463800-74474200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:74464200-74476400	Enhancers	Stomach Mucosa	stomach
3	chr4:74464200-74477200	Enhancers	Fetal Intestine Small	intestine
4	chr4:74465000-74475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:74465400-74483000	Weak transcription	Esophagus	oesophagus
6	chr4:74465800-74473000	Weak transcription	NHEK	skin
7	chr4:74465800-74476000	Weak transcription	Placenta	Placenta
8	chr4:74466800-74474600	Weak transcription	Fetal Kidney	kidney
9	chr4:74467000-74474400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:74469400-74474400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:74469800-74473000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:74469800-74473000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:74469800-74474400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:74469800-74474400	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:74469800-74474600	Weak transcription	Liver	Liver
16	chr4:74469800-74477200	Enhancers	HepG2	liver
17	chr4:74470000-74473000	Weak transcription	Osteobl	bone
18	chr4:74470000-74474400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:74470000-74475400	Weak transcription	Fetal Lung	lung
20	chr4:74470000-74475400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:74470800-74473600	Enhancers	Primary B cells from peripheral blood	blood
22	chr4:74470800-74473600	Enhancers	Primary T cells from cord blood	blood
23	chr4:74470800-74476000	Enhancers	Fetal Intestine Large	intestine
24	chr4:74471000-74473200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:74471200-74473400	Enhancers	Primary B cells from cord blood	blood
26	chr4:74471600-74473400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:74471800-74473200	Enhancers	Small Intestine	intestine
28	chr4:74471800-74473400	Enhancers	Duodenum Mucosa	Duodenum
29	chr4:74472000-74473400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:74472000-74473400	Flanking Active TSS	GM12878-XiMat	blood
31	chr4:74472000-74473600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr4:74472000-74473800	Enhancers	Pancreas	Pancrea
33	chr4:74472200-74473600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr4:74472200-74474400	Enhancers	HMEC	breast
35	chr4:74472200-74485600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:74472400-74473200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:74472400-74473600	Enhancers	Fetal Thymus	thymus
38	chr4:74472400-74473800	Enhancers	HSMM	muscle
39	chr4:74472400-74477800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:74472600-74473200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:74472600-74473200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:74472600-74473200	Enhancers	Primary T cells fromperipheralblood	blood
43	chr4:74472600-74473200	Enhancers	Gastric	stomach
44	chr4:74472600-74473400	Flanking Active TSS	Dnd41	blood
45	chr4:74472600-74473600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr4:74472600-74473800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr4:74472600-74473800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:74472800-74473000	Flanking Active TSS	A549	lung
49	chr4:74472800-74473600	Enhancers	Thymus	Thymus
50	chr4:74472800-74474400	Weak transcription	Colonic Mucosa	Colon

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