Variant report

Variant	rs6656270
Chromosome Location	chr1:94157942-94157943
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94157790..94160222-chr1:94162469..94164746,2	K562	blood:
2	chr1:94150767..94155477-chr1:94157317..94159691,6	MCF-7	breast:
3	chr1:94155482..94158108-chr1:94158298..94159842,2	MCF-7	breast:
4	chr1:94146120..94150945-chr1:94154288..94160235,6	MCF-7	breast:
5	chr1:94157694..94160126-chr1:94167875..94169422,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1011903	1.00[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1011904	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11164961	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11164962	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11164963	1.00[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12057736	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12059154	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12079723	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12084853	1.00[CEU][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12092517	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1567791	1.00[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs236284	0.85[CEU][hapmap]
rs236287	0.85[CEU][hapmap]
rs61781002	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6541386	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6541387	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6541388	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6541389	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6657709	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6660740	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]
rs6675484	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6684568	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6694536	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6701871	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6702036	1.00[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6704479	1.00[CEU][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7513130	0.82[CEU][hapmap]
rs7519952	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs955470	0.93[AMR][1000 genomes];0.89[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
rs6656270	SNORD21	cis	cerebellum	SCAN
rs6656270	F3	cis	cerebellum	SCAN

Chromatin state (count:75 , 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	chr1:94154600-94159000	Enhancers	Duodenum Mucosa	Duodenum
5	chr1:94155200-94159400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:94155200-94159800	Enhancers	Fetal Intestine Large	intestine
7	chr1:94155200-94159800	Enhancers	HepG2	liver
8	chr1:94155400-94158200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:94155400-94158200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:94155600-94158200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:94155600-94171000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:94156200-94158000	Enhancers	HSMM	muscle
13	chr1:94156400-94158200	Enhancers	HMEC	breast
14	chr1:94156400-94161200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:94156400-94162400	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:94156600-94158000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:94156600-94159000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:94156600-94159600	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:94156600-94159600	Enhancers	Fetal Thymus	thymus
20	chr1:94156600-94160600	Enhancers	Fetal Muscle Leg	muscle
21	chr1:94156600-94161600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:94156600-94162200	Enhancers	Placenta	Placenta
23	chr1:94156800-94158000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:94156800-94158200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:94156800-94158200	Enhancers	GM12878-XiMat	blood
26	chr1:94156800-94158800	Enhancers	Adipose Nuclei	Adipose
27	chr1:94156800-94159200	Enhancers	Thymus	Thymus
28	chr1:94156800-94159400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr1:94156800-94160200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:94156800-94161000	Enhancers	HSMMtube	muscle
31	chr1:94156800-94161400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:94156800-94162200	Enhancers	Primary B cells from cord blood	blood
33	chr1:94157000-94160600	Enhancers	Fetal Muscle Trunk	muscle
34	chr1:94157000-94160800	Enhancers	Lung	lung
35	chr1:94157200-94158000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr1:94157200-94158000	Enhancers	Aorta	Aorta
37	chr1:94157200-94158000	Enhancers	Stomach Smooth Muscle	stomach
38	chr1:94157200-94158200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:94157200-94158200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:94157200-94158600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:94157200-94159000	Enhancers	Fetal Kidney	kidney
42	chr1:94157200-94159000	Enhancers	Fetal Lung	lung
43	chr1:94157200-94160400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:94157200-94165400	Weak transcription	Pancreas	Pancrea
45	chr1:94157400-94158000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:94157400-94158000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:94157400-94158000	Weak transcription	Small Intestine	intestine
48	chr1:94157400-94158200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:94157400-94158200	Enhancers	Osteobl	bone
50	chr1:94157400-94159800	Flanking Active TSS	A549	lung

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