Variant report

Variant	rs666779
Chromosome Location	chr1:85410544-85410545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:85410006..85410936-chr1:85495368..85495874,2	MCF-7	breast:
2	chr1:84382101..84384733-chr1:85409125..85411327,2	K562	blood:
3	chr1:85410240..85410751-chr1:85493199..85493798,2	MCF-7	breast:
4	chr1:85410272..85411869-chr1:85493014..85494336,19	MCF-7	breast:
5	chr1:85410252..85411181-chr1:85719873..85720677,4	K562	blood:
6	chr1:85409879..85410688-chr1:85705752..85706654,2	K562	blood:
7	chr1:85410128..85411315-chr1:85490122..85491874,8	MCF-7	breast:
8	chr1:85410308..85411228-chr1:85705720..85706844,7	MCF-7	breast:
9	chr1:85410118..85411009-chr1:85725007..85725639,2	MCF-7	breast:
10	chr1:85410258..85411298-chr1:85720149..85720894,4	MCF-7	breast:
11	chr1:85410065..85411348-chr1:85724616..85726527,9	K562	blood:
12	chr1:85410353..85411305-chr1:85719958..85721105,6	MCF-7	breast:
13	chr1:85409622..85411011-chr1:85492995..85494617,8	MCF-7	breast:
14	chr1:85410326..85411124-chr1:85544047..85544918,2	MCF-7	breast:
15	chr1:85410011..85410751-chr1:85491092..85491875,2	MCF-7	breast:
16	chr1:85410009..85411013-chr1:85724647..85725830,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162642	Chromatin interaction
ENSG00000055732	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12064092	0.86[YRI][hapmap]
rs12118848	0.83[CEU][hapmap]
rs12120635	0.90[CEU][hapmap]
rs12402639	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs12402681	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs1325277	0.94[CEU][hapmap];0.84[CHB][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55873701	0.85[EUR][1000 genomes]
rs570564	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs589332	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs621003	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639500	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs650357	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85396400-85410600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:85396600-85410800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:85400800-85410800	Weak transcription	Fetal Lung	lung
4	chr1:85402000-85419600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:85403800-85410800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:85405000-85413200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:85405200-85413000	Weak transcription	Esophagus	oesophagus
8	chr1:85406600-85410800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:85406600-85410800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:85406600-85410800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:85406800-85410800	Weak transcription	HMEC	breast
12	chr1:85406800-85412000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:85410200-85410600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:85410200-85410600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr1:85410200-85410600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:85410200-85410600	Enhancers	Dnd41	blood
17	chr1:85410200-85410600	Enhancers	GM12878-XiMat	blood
18	chr1:85410200-85410800	Enhancers	Primary B cells from peripheral blood	blood
19	chr1:85410200-85410800	Enhancers	Fetal Thymus	thymus
20	chr1:85410400-85410600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr1:85410400-85410600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr1:85410400-85410600	Enhancers	Primary hematopoietic stem cells	blood
23	chr1:85410400-85410600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:85410400-85410600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr1:85410400-85410600	Enhancers	Colon Smooth Muscle	Colon
26	chr1:85410400-85410600	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr1:85410400-85410800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:85410400-85410800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:85410400-85410800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr1:85410400-85410800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:85410400-85410800	Enhancers	Liver	Liver
32	chr1:85410400-85410800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:85410400-85410800	Flanking Active TSS	Stomach Mucosa	stomach
34	chr1:85410400-85410800	Enhancers	NHEK	skin
35	chr1:85410400-85411200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr1:85410400-85411400	Active TSS	Monocytes-CD14+_RO01746	blood
37	chr1:85410400-85412000	Active TSS	Stomach Smooth Muscle	stomach
38	chr1:85410400-85413800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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