Variant report

Variant	rs17197341
Chromosome Location	chr8:103889712-103889713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59476878..59479455-chr8:103889227..103891681,2	MCF-7	breast:
2	chr8:103883028..103885294-chr8:103888959..103891854,2	MCF-7	breast:
3	chr8:103880964..103882727-chr8:103887740..103890227,2	MCF-7	breast:
4	chr8:103889506..103892045-chr8:103897446..103899606,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP6V1C1-8	chr8:103888226-103889957	ucscGeneNc_uc003ykw_1

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000121068	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1019975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10505040	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12544232	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12546193	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12546479	0.89[AMR][1000 genomes]
rs12546634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12546960	0.89[AMR][1000 genomes]
rs12547200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12547652	0.89[AMR][1000 genomes]
rs12548786	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12549011	0.89[AMR][1000 genomes]
rs12549073	0.89[AMR][1000 genomes]
rs12550185	0.88[AMR][1000 genomes]
rs13123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17197736	0.89[AMR][1000 genomes]
rs17198079	0.85[AMR][1000 genomes]
rs17775450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17775510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2011262	0.81[EUR][1000 genomes]
rs2137339	0.89[AMR][1000 genomes]
rs2304348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2304349	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2388369	0.89[AMR][1000 genomes]
rs2388370	0.89[AMR][1000 genomes]
rs28542883	0.86[ASN][1000 genomes]
rs4734670	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4734672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4734673	0.89[AMR][1000 genomes]
rs4734674	0.89[AMR][1000 genomes]
rs4734676	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734678	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56854051	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522574	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62522599	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62522602	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62522603	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62522615	0.89[AMR][1000 genomes]
rs62522616	0.89[AMR][1000 genomes]
rs62522617	0.89[AMR][1000 genomes]
rs62522618	0.89[AMR][1000 genomes]
rs62522619	0.89[AMR][1000 genomes]
rs62522620	0.89[AMR][1000 genomes]
rs62522621	0.89[AMR][1000 genomes]
rs62522622	0.89[AMR][1000 genomes]
rs62522623	0.86[AMR][1000 genomes]
rs62522624	0.89[AMR][1000 genomes]
rs62522626	0.89[AMR][1000 genomes]
rs62526529	0.89[AMR][1000 genomes]
rs62526533	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62526534	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62526538	0.92[ASN][1000 genomes]
rs62526539	0.92[ASN][1000 genomes]
rs6468846	0.92[ASN][1000 genomes]
rs6998032	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs6999267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6999525	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7016840	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7821657	0.86[ASN][1000 genomes]
rs7843670	0.82[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	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1021898	chr8:103767324-103922482	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv465751	chr8:103817106-103894326	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh 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	62 gene(s)	inside rSNPs	diseases
4	nsv611822	chr8:103817106-103894326	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv891245	chr8:103838004-103907253	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103877000-103906800	Weak transcription	Gastric	stomach
2	chr8:103877200-103893200	Weak transcription	Pancreas	Pancrea
3	chr8:103877800-103902000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr8:103877800-103906400	Weak transcription	HSMMtube	muscle
5	chr8:103878000-103906400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr8:103878000-103908800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr8:103878200-103892800	Weak transcription	Fetal Muscle Leg	muscle
8	chr8:103878200-103897400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr8:103878200-103906600	Weak transcription	Ovary	ovary
10	chr8:103878400-103897200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:103878600-103892800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:103878600-103897600	Weak transcription	Fetal Brain Female	brain
13	chr8:103878800-103893400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr8:103878800-103895600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr8:103878800-103899800	Weak transcription	Esophagus	oesophagus
16	chr8:103879000-103893000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr8:103879200-103922000	Weak transcription	Fetal Intestine Small	intestine
18	chr8:103881000-103899000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr8:103882800-103906600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr8:103883200-103893200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr8:103884400-103894000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:103884400-103900600	Weak transcription	Aorta	Aorta
23	chr8:103884600-103897400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:103886600-103892800	Weak transcription	Placenta	Placenta
25	chr8:103886800-103898800	Weak transcription	Fetal Thymus	thymus
26	chr8:103887800-103892800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr8:103887800-103893200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr8:103889000-103890200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr8:103889200-103893400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:103889400-103889800	Enhancers	Brain Substantia Nigra	brain
31	chr8:103889600-103889800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr8:103889600-103889800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr8:103889600-103890000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
34	chr8:103889600-103890000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr8:103889600-103890000	Enhancers	Brain Angular Gyrus	brain
36	chr8:103889600-103890000	Enhancers	Brain Anterior Caudate	brain
37	chr8:103889600-103890000	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr8:103889600-103890000	Enhancers	Psoas Muscle	Psoas
39	chr8:103889600-103890200	Enhancers	Brain Cingulate Gyrus	brain
40	chr8:103889600-103890200	Enhancers	Brain Inferior Temporal Lobe	brain

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