Variant report

Variant	rs6660740
Chromosome Location	chr1:94157572-94157573
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94150767..94155477-chr1:94157317..94159691,6	MCF-7	breast:
2	chr1:94155482..94158108-chr1:94158298..94159842,2	MCF-7	breast:
3	chr1:94146120..94150945-chr1:94154288..94160235,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1011903	1.00[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1011904	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164961	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164962	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11164963	1.00[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12057736	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079723	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12084853	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12092517	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12568405	1.00[JPT][hapmap]
rs1567791	1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs236284	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs236285	0.84[ASN][1000 genomes]
rs236287	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs236343	0.88[JPT][hapmap]
rs236344	0.86[MEX][hapmap]
rs3767979	0.88[JPT][hapmap]
rs61781002	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6541386	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6541387	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6541388	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6541389	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6656270	1.00[CEU][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6657709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675484	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6684568	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6694536	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701871	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6702036	1.00[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6704479	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7513130	0.85[CEU][hapmap]
rs7519952	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs955470	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9659100	0.80[EUR][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	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6660740	SNORD21	cis	cerebellum	SCAN
rs6660740	F3	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94148200-94167200	Weak transcription	Right Atrium	heart
2	chr1:94152200-94159000	Enhancers	Fetal Intestine Small	intestine
3	chr1:94153800-94171600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:94154600-94157600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:94154600-94159000	Enhancers	Duodenum Mucosa	Duodenum
6	chr1:94155200-94159400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:94155200-94159800	Enhancers	Fetal Intestine Large	intestine
8	chr1:94155200-94159800	Enhancers	HepG2	liver
9	chr1:94155400-94157600	Enhancers	Hela-S3	cervix
10	chr1:94155400-94157600	Weak transcription	NH-A	brain
11	chr1:94155400-94157800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:94155400-94158200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:94155400-94158200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:94155600-94158200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:94155600-94171000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:94156200-94157600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:94156200-94157800	Enhancers	NHDF-Ad	bronchial
18	chr1:94156200-94158000	Enhancers	HSMM	muscle
19	chr1:94156400-94157600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:94156400-94157800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:94156400-94158200	Enhancers	HMEC	breast
22	chr1:94156400-94161200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:94156400-94162400	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:94156600-94157600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:94156600-94157800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:94156600-94157800	Enhancers	NHEK	skin
27	chr1:94156600-94158000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:94156600-94159000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:94156600-94159600	Enhancers	Primary hematopoietic stem cells	blood
30	chr1:94156600-94159600	Enhancers	Fetal Thymus	thymus
31	chr1:94156600-94160600	Enhancers	Fetal Muscle Leg	muscle
32	chr1:94156600-94161600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:94156600-94162200	Enhancers	Placenta	Placenta
34	chr1:94156800-94157600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr1:94156800-94157600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr1:94156800-94157800	Enhancers	NHLF	lung
37	chr1:94156800-94158000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:94156800-94158200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:94156800-94158200	Enhancers	GM12878-XiMat	blood
40	chr1:94156800-94158800	Enhancers	Adipose Nuclei	Adipose
41	chr1:94156800-94159200	Enhancers	Thymus	Thymus
42	chr1:94156800-94159400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr1:94156800-94160200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:94156800-94161000	Enhancers	HSMMtube	muscle
45	chr1:94156800-94161400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:94156800-94162200	Enhancers	Primary B cells from cord blood	blood
47	chr1:94157000-94157600	Weak transcription	Esophagus	oesophagus
48	chr1:94157000-94157600	Enhancers	Spleen	Spleen
49	chr1:94157000-94160600	Enhancers	Fetal Muscle Trunk	muscle
50	chr1:94157000-94160800	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links