Variant report

Variant	rs6658042
Chromosome Location	chr1:159909242-159909243
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	chr1:159907235..159909524-chr1:159933511..159935771,2	MCF-7	breast:
2	chr1:159907782..159910427-chr1:159933319..159935593,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10752634	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10797054	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10797055	0.93[ASN][1000 genomes]
rs10908750	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12139175	0.89[ASN][1000 genomes]
rs1320566	0.89[ASN][1000 genomes]
rs1934075	0.82[EUR][1000 genomes]
rs6703466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524321	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7526647	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv524006	chr1:159886422-159923111	Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159905400-159909600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:159905400-159909800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:159905800-159911400	Enhancers	Placenta	Placenta
4	chr1:159905800-159913600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:159906000-159909400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr1:159906000-159910600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:159906000-159911000	Weak transcription	Brain Germinal Matrix	brain
8	chr1:159906400-159909600	Genic enhancers	NHEK	skin
9	chr1:159906600-159909800	Enhancers	Small Intestine	intestine
10	chr1:159906800-159910200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:159907000-159915200	Weak transcription	Gastric	stomach
12	chr1:159907400-159909600	Weak transcription	A549	lung
13	chr1:159907400-159910600	Weak transcription	Fetal Brain Male	brain
14	chr1:159907400-159911400	Weak transcription	Thymus	Thymus
15	chr1:159907600-159909400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:159907600-159909600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:159907600-159909800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:159907600-159909800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:159907600-159909800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:159907600-159910000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:159907600-159910600	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:159907800-159910400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:159908000-159909600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:159908000-159909600	Enhancers	Fetal Intestine Large	intestine
25	chr1:159908000-159910200	Genic enhancers	Fetal Intestine Small	intestine
26	chr1:159908200-159911000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:159908200-159911000	Weak transcription	Fetal Stomach	stomach
28	chr1:159908400-159909600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:159908400-159909800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:159908400-159910200	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr1:159908400-159913200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:159908400-159913800	Weak transcription	Fetal Heart	heart
33	chr1:159908400-159914600	Enhancers	Stomach Mucosa	stomach
34	chr1:159908400-159915200	Weak transcription	Spleen	Spleen
35	chr1:159908600-159910000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:159908600-159910000	Weak transcription	Fetal Brain Female	brain
37	chr1:159908600-159910400	Weak transcription	Fetal Thymus	thymus
38	chr1:159908600-159910400	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr1:159908600-159911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:159908600-159911000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:159908600-159911200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:159908600-159913400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:159908600-159914000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:159908600-159914200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:159908800-159909400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr1:159908800-159910000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:159908800-159911600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:159909000-159910000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:159909000-159910000	Weak transcription	Liver	Liver
50	chr1:159909000-159910000	Weak transcription	Esophagus	oesophagus

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