Variant report

Variant	rs6657709
Chromosome Location	chr1:94157041-94157042
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94144346..94147845-chr1:94153555..94157054,4	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: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1011903	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1011904	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11164961	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11164962	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164963	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12057736	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059154	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079723	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12084853	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12092517	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12568405	1.00[JPT][hapmap]
rs1567791	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs236284	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs236285	0.84[ASN][1000 genomes]
rs236287	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs236343	0.88[JPT][hapmap]
rs3767979	0.88[JPT][hapmap]
rs61781002	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6541386	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6541387	0.88[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6541388	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6541389	0.88[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6656270	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6660740	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];0.95[EUR][1000 genomes]
rs6684568	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6694536	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701871	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6702036	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6704479	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7519952	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs955470	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9659100	0.82[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

No data

Chromatin state (count:65 , 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	chr1:94152400-94157200	Weak transcription	Small Intestine	intestine
4	chr1:94152600-94157400	Weak transcription	HUVEC	blood vessel
5	chr1:94153800-94171600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:94154600-94157600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:94154600-94159000	Enhancers	Duodenum Mucosa	Duodenum
8	chr1:94155000-94157400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:94155200-94157400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:94155200-94159400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:94155200-94159800	Enhancers	Fetal Intestine Large	intestine
12	chr1:94155200-94159800	Enhancers	HepG2	liver
13	chr1:94155400-94157600	Enhancers	Hela-S3	cervix
14	chr1:94155400-94157600	Weak transcription	NH-A	brain
15	chr1:94155400-94157800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:94155400-94158200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:94155400-94158200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:94155600-94157200	Weak transcription	Fetal Kidney	kidney
19	chr1:94155600-94158200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:94155600-94171000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:94155800-94157400	Enhancers	A549	lung
22	chr1:94156200-94157600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:94156200-94157800	Enhancers	NHDF-Ad	bronchial
24	chr1:94156200-94158000	Enhancers	HSMM	muscle
25	chr1:94156400-94157600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:94156400-94157800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:94156400-94158200	Enhancers	HMEC	breast
28	chr1:94156400-94161200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:94156400-94162400	Enhancers	Primary B cells from peripheral blood	blood
30	chr1:94156600-94157200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:94156600-94157400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr1:94156600-94157400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:94156600-94157600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:94156600-94157800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:94156600-94157800	Enhancers	NHEK	skin
36	chr1:94156600-94158000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:94156600-94159000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:94156600-94159600	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:94156600-94159600	Enhancers	Fetal Thymus	thymus
40	chr1:94156600-94160600	Enhancers	Fetal Muscle Leg	muscle
41	chr1:94156600-94161600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:94156600-94162200	Enhancers	Placenta	Placenta
43	chr1:94156800-94157200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr1:94156800-94157200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:94156800-94157200	Enhancers	Pancreas	Pancrea
46	chr1:94156800-94157400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:94156800-94157600	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr1:94156800-94157600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:94156800-94157800	Enhancers	NHLF	lung
50	chr1:94156800-94158000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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