Variant report

Variant	rs17776569
Chromosome Location	chr8:103890807-103890808
allele	G/T
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	chr8:103889506..103892045-chr8:103897446..103899606,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP6V1C1-8	chr8:103890338-103891379	ucscGeneNc_uc003ykw_1

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

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1019976	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1062048	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10955294	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs17776600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1802539	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1806300	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897787	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1982111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1991928	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2247355	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2436849	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2436851	0.81[ASN][1000 genomes]
rs2436856	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2436861	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2513875	0.95[AFR][1000 genomes]
rs2513876	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2513877	0.96[EUR][1000 genomes]
rs2513911	0.81[CHB][hapmap];0.87[YRI][hapmap]
rs2513912	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2513915	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2513917	0.81[ASN][1000 genomes]
rs2513920	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2513923	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2513936	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2570941	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2570945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2570951	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2570952	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2679736	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2679737	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2679740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2679745	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2679747	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2679750	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2679753	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2916559	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs3018943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3018954	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs34157576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35656046	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565720	0.94[CHB][hapmap]
rs581610	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs601088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677406	0.82[ASN][1000 genomes]
rs688791	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs974758	0.82[AFR][1000 genomes];0.83[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:42 , 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	chr8:103889200-103893400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr8:103889800-103899000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr8:103889800-103906200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr8:103889800-103906400	Weak transcription	Brain Substantia Nigra	brain
32	chr8:103890000-103893200	Weak transcription	Psoas Muscle	Psoas
33	chr8:103890000-103893400	Weak transcription	Right Atrium	heart
34	chr8:103890000-103899000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr8:103890000-103906400	Weak transcription	Brain Hippocampus Middle	brain
36	chr8:103890000-103906600	Weak transcription	Brain Anterior Caudate	brain
37	chr8:103890000-103906600	Weak transcription	Right Ventricle	heart
38	chr8:103890200-103892600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr8:103890200-103900400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr8:103890200-103906400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr8:103890600-103891200	Weak transcription	Fetal Stomach	stomach
42	chr8:103890800-103893200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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