Variant report

Variant	rs1880456
Chromosome Location	chr7:17887646-17887647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:17886526..17888087-chr7:17888537..17890269,2	MCF-7	breast:
2	chr7:17886413..17888051-chr7:17895636..17897500,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10228026	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs10229298	0.91[YRI][hapmap]
rs10230644	0.84[YRI][hapmap]
rs10231119	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10231226	0.84[YRI][hapmap]
rs10231837	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs10234457	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs10237285	0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs10252726	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10274155	0.84[YRI][hapmap]
rs10278523	0.90[YRI][hapmap]
rs10282332	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10282571	0.84[YRI][hapmap]
rs11975603	0.82[YRI][hapmap]
rs17138311	0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs17138375	0.84[YRI][hapmap]
rs17138395	0.90[YRI][hapmap]
rs17138405	0.84[YRI][hapmap]
rs28566938	0.84[AFR][1000 genomes]
rs59412224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308167	0.84[AFR][1000 genomes]
rs7797640	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869352	chr7:17237983-17932878	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1021524	chr7:17251148-17963307	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv534309	chr7:17254118-17932878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv533938	chr7:17254118-18040301	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1024398	chr7:17630148-18545073	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
6	nsv538764	chr7:17630148-18545073	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
7	esv1802979	chr7:17816528-17908546	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv830913	chr7:17848480-18034218	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv1792752	chr7:17853983-17908546	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1026629	chr7:17862477-18362404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1025023	chr7:17865796-18357630	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17834000-17887800	Weak transcription	Right Ventricle	heart
2	chr7:17834800-17888800	Weak transcription	Brain Substantia Nigra	brain
3	chr7:17839000-17932600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:17841200-17902600	Weak transcription	Brain Anterior Caudate	brain
5	chr7:17846000-17900600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:17852600-17887800	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:17852600-17896000	Weak transcription	Fetal Kidney	kidney
8	chr7:17852600-17902800	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:17852800-17890200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr7:17852800-17895000	Weak transcription	Brain Germinal Matrix	brain
11	chr7:17853600-17888000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr7:17853800-17914000	Weak transcription	Hela-S3	cervix
13	chr7:17854000-17887800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr7:17854000-17900800	Weak transcription	K562	blood
15	chr7:17862800-17888000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:17862800-17894800	Weak transcription	Psoas Muscle	Psoas
17	chr7:17872600-17889400	Weak transcription	Fetal Brain Male	brain
18	chr7:17876200-17901000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:17877600-17902600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:17877800-17917400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:17878000-17896000	Weak transcription	Brain Angular Gyrus	brain
22	chr7:17878200-17918400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr7:17879400-17887800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:17879400-17896000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:17879400-17896000	Weak transcription	Placenta	Placenta
26	chr7:17879600-17888400	Weak transcription	NH-A	brain
27	chr7:17879800-17889000	Weak transcription	Osteobl	bone
28	chr7:17879800-17911000	Weak transcription	HepG2	liver
29	chr7:17881000-17887800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:17881000-17887800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr7:17881000-17889200	Weak transcription	HSMMtube	muscle
32	chr7:17881000-17892400	Weak transcription	Fetal Lung	lung
33	chr7:17881000-17897000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr7:17881000-17899000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:17881000-17899600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr7:17881000-17901200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr7:17881000-17903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr7:17881200-17888400	Weak transcription	Fetal Heart	heart
39	chr7:17881200-17895600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:17881400-17903000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr7:17882000-17895200	Weak transcription	A549	lung
42	chr7:17882200-17896400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr7:17883200-17888000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr7:17883400-17888200	Weak transcription	HSMM	muscle
45	chr7:17883400-17889400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:17883800-17894200	Weak transcription	GM12878-XiMat	blood
47	chr7:17884000-17896000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:17884200-17888200	Weak transcription	Dnd41	blood
49	chr7:17884200-17891800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr7:17884400-17887800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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