Variant report

Variant	rs891545
Chromosome Location	chr7:128866616-128866617
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128865235..128868002-chr7:128877453..128879844,2	MCF-7	breast:
2	chr7:128864343..128867175-chr7:129072018..129074296,2	K562	blood:
3	chr7:128866260..128868499-chr7:128899979..128902017,2	K562	blood:
4	chr7:128694062..128696467-chr7:128864942..128866876,2	K562	blood:
5	chr7:128862977..128866028-chr7:128866480..128869690,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064419	Chromatin interaction
ENSG00000158467	Chromatin interaction
ENSG00000128578	Chromatin interaction
ENSG00000230359	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1000676	0.81[JPT][hapmap]
rs10248810	0.95[CEU][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10257620	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10954224	0.94[ASN][1000 genomes]
rs10954226	0.87[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs10954230	0.81[JPT][hapmap]
rs11769045	0.83[ASN][1000 genomes]
rs11979476	0.82[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs12111832	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12112374	0.82[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs12216567	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12534372	0.81[JPT][hapmap]
rs12540568	0.81[JPT][hapmap]
rs12667132	0.81[JPT][hapmap]
rs13226649	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13235668	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13235749	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13238161	0.92[ASN][1000 genomes]
rs1473236	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1526900	0.86[JPT][hapmap]
rs1559486	0.91[JPT][hapmap]
rs1880854	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2012919	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2141075	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2402944	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2566876	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2566877	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2566885	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2566886	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2694572	0.87[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2694574	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs2718083	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2718084	0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2718089	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2718093	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2718096	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2718115	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896415	0.93[ASN][1000 genomes]
rs4728163	0.81[JPT][hapmap]
rs4731566	0.94[ASN][1000 genomes]
rs4731568	0.87[ASN][1000 genomes]
rs4731572	0.81[JPT][hapmap]
rs55638303	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62480596	0.94[ASN][1000 genomes]
rs6467233	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467237	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6467240	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6467241	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6467242	0.82[EUR][1000 genomes]
rs66970518	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67820265	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67853067	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68184415	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6942756	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6966595	0.82[CEU][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.89[MKK][hapmap]
rs6967464	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6980385	0.82[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs721691	0.88[ASN][1000 genomes]
rs7780886	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7782348	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7788327	0.95[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7794622	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7811141	0.89[ASN][1000 genomes]
rs822038	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs822040	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs963465	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9640854	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9641846	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[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];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9641849	0.82[ASN][1000 genomes]

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	nsv831127	chr7:128716256-128874691	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1031284	chr7:128866118-128910506	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs891545	COPG2	cis	cerebellum	SCAN
rs891545	KCP	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128863600-128867200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:128865400-128866800	Flanking Active TSS	Dnd41	blood
3	chr7:128865600-128866800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr7:128865600-128866800	Flanking Active TSS	Fetal Brain Female	brain
5	chr7:128865800-128867400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:128865800-128872800	Weak transcription	Lung	lung
7	chr7:128866000-128866800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
8	chr7:128866000-128866800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
9	chr7:128866000-128866800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr7:128866000-128866800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:128866000-128867000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr7:128866000-128867000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr7:128866000-128867200	Enhancers	Primary B cells from peripheral blood	blood
14	chr7:128866000-128867400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr7:128866000-128867600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:128866000-128867600	Enhancers	Small Intestine	intestine
17	chr7:128866000-128873600	Weak transcription	Pancreas	Pancrea
18	chr7:128866000-128874400	Weak transcription	HSMM	muscle
19	chr7:128866000-128880000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:128866000-128902200	Weak transcription	Gastric	stomach
21	chr7:128866200-128866800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr7:128866200-128866800	Enhancers	Fetal Heart	heart
23	chr7:128866200-128866800	Enhancers	Fetal Intestine Small	intestine
24	chr7:128866200-128866800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr7:128866200-128867000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr7:128866200-128867000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr7:128866200-128867800	Flanking Active TSS	NHEK	skin
28	chr7:128866200-128868800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:128866200-128898600	Weak transcription	Thymus	Thymus
30	chr7:128866400-128866800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr7:128866400-128866800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:128866400-128866800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr7:128866400-128866800	Enhancers	Liver	Liver
34	chr7:128866400-128866800	Active TSS	Brain Hippocampus Middle	brain
35	chr7:128866400-128866800	Enhancers	Fetal Kidney	kidney
36	chr7:128866400-128866800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr7:128866400-128866800	Flanking Active TSS	HMEC	breast
38	chr7:128866400-128867000	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr7:128866400-128867000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:128866400-128867000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr7:128866400-128867000	Enhancers	A549	lung
42	chr7:128866400-128867000	Enhancers	K562	blood
43	chr7:128866400-128867200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr7:128866400-128867200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr7:128866400-128867200	Weak transcription	Psoas Muscle	Psoas
46	chr7:128866400-128867400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr7:128866400-128867400	Weak transcription	Stomach Mucosa	stomach
48	chr7:128866400-128867800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:128866400-128868200	Enhancers	HepG2	liver
50	chr7:128866400-128869400	Weak transcription	HSMMtube	muscle

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