Variant report

Variant	rs58980183
Chromosome Location	chr6:56629733-56629734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56628856..56630508-chr6:56635256..56637905,2	MCF-7	breast:
2	chr6:56575771..56576356-chr6:56629025..56629997,2	MCF-7	breast:
3	chr6:56628605..56630387-chr6:56707812..56709919,2	MCF-7	breast:
4	chr6:56625069..56627235-chr6:56628459..56631328,2	K562	blood:
5	chr6:56610420..56612281-chr6:56629163..56631061,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000231441	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10498812	0.86[EUR][1000 genomes]
rs10498813	0.86[EUR][1000 genomes]
rs11756551	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11970648	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13190784	0.87[ASN][1000 genomes]
rs13190854	0.85[EUR][1000 genomes]
rs13191826	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13192540	0.82[EUR][1000 genomes]
rs13192931	0.82[EUR][1000 genomes]
rs13194625	0.86[EUR][1000 genomes]
rs13194904	0.90[EUR][1000 genomes]
rs13195601	0.85[EUR][1000 genomes]
rs13198204	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13198399	0.83[AMR][1000 genomes]
rs13200166	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13200559	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13200768	0.95[EUR][1000 genomes]
rs13200868	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201639	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13201733	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13203000	0.81[AMR][1000 genomes]
rs13203148	0.86[EUR][1000 genomes]
rs13203327	0.92[EUR][1000 genomes]
rs13203681	0.82[EUR][1000 genomes]
rs13204466	0.95[EUR][1000 genomes]
rs13205667	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13207768	0.81[EUR][1000 genomes]
rs13208409	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13211879	0.85[EUR][1000 genomes]
rs13214135	0.83[AMR][1000 genomes]
rs13217390	0.81[AMR][1000 genomes]
rs13218913	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13220618	0.86[EUR][1000 genomes]
rs13220628	0.86[EUR][1000 genomes]
rs13220851	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1610157	0.81[EUR][1000 genomes]
rs16888171	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16888186	1.00[ASN][1000 genomes]
rs17684730	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684748	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684772	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684784	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17684802	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17684878	0.82[EUR][1000 genomes]
rs17684884	0.82[EUR][1000 genomes]
rs17751966	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17751977	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17752002	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17752046	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17752106	0.82[EUR][1000 genomes]
rs1903332	1.00[ASN][1000 genomes]
rs3002010	0.82[AMR][1000 genomes]
rs3002011	0.82[AMR][1000 genomes]
rs34171958	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34228698	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34359353	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34425815	0.88[EUR][1000 genomes]
rs34455199	0.81[AMR][1000 genomes]
rs34465210	0.81[AMR][1000 genomes]
rs34500949	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34520435	0.89[EUR][1000 genomes]
rs34566275	0.81[AMR][1000 genomes]
rs34587484	0.81[AMR][1000 genomes]
rs34612783	0.95[EUR][1000 genomes]
rs34614087	0.85[EUR][1000 genomes]
rs34623351	0.81[AMR][1000 genomes]
rs34640766	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34803237	0.81[AMR][1000 genomes]
rs34866877	0.85[EUR][1000 genomes]
rs34896026	0.85[EUR][1000 genomes]
rs34966024	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35073881	0.82[EUR][1000 genomes]
rs35080938	0.82[EUR][1000 genomes]
rs35081015	0.86[EUR][1000 genomes]
rs35225175	0.86[EUR][1000 genomes]
rs35242294	0.81[EUR][1000 genomes]
rs35251663	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35407078	0.85[EUR][1000 genomes]
rs35439100	0.85[EUR][1000 genomes]
rs35440408	1.00[ASN][1000 genomes]
rs35440822	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35461301	0.85[EUR][1000 genomes]
rs35566812	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35609883	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35642890	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35696739	0.90[EUR][1000 genomes]
rs35828379	0.82[EUR][1000 genomes]
rs35851452	0.85[EUR][1000 genomes]
rs35873865	0.94[EUR][1000 genomes]
rs35876418	0.81[AMR][1000 genomes]
rs35886823	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35986172	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36022925	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36037734	0.90[EUR][1000 genomes]
rs36094082	0.82[EUR][1000 genomes]
rs4299824	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4348308	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4371846	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4415160	0.85[EUR][1000 genomes]
rs4457154	0.90[EUR][1000 genomes]
rs4532444	0.86[EUR][1000 genomes]
rs4587171	0.87[EUR][1000 genomes]
rs56368885	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59432342	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60163288	1.00[ASN][1000 genomes]
rs61601344	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411366	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62411367	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62411372	0.95[EUR][1000 genomes]
rs62411375	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62411376	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6904535	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905603	0.81[EUR][1000 genomes]
rs6905658	0.87[ASN][1000 genomes]
rs6910414	1.00[ASN][1000 genomes]
rs6914293	0.81[EUR][1000 genomes]
rs6918949	0.81[EUR][1000 genomes]
rs6925518	0.87[ASN][1000 genomes]
rs6926742	0.87[ASN][1000 genomes]
rs6928104	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6934714	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71564854	0.93[EUR][1000 genomes]
rs71564855	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71564856	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71564861	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71564863	0.82[EUR][1000 genomes]
rs7758867	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761501	0.82[EUR][1000 genomes]
rs7761729	0.81[EUR][1000 genomes]
rs7771085	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7775182	0.85[EUR][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56621400-56634200	Weak transcription	Spleen	Spleen
2	chr6:56622400-56637600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:56622800-56631000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:56623000-56631000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:56623200-56631000	Weak transcription	Fetal Lung	lung
6	chr6:56623600-56631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:56623600-56637200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:56623600-56637600	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:56623800-56630200	Weak transcription	HSMMtube	muscle
10	chr6:56623800-56630400	Weak transcription	Fetal Stomach	stomach
11	chr6:56625200-56637800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:56625400-56631400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:56625600-56637000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:56625600-56649800	Weak transcription	Brain Germinal Matrix	brain
15	chr6:56625800-56637000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:56626400-56631200	Weak transcription	HMEC	breast
17	chr6:56626400-56631200	Weak transcription	NHEK	skin
18	chr6:56626400-56637200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:56626600-56636000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:56627200-56637400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:56627800-56633000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr6:56627800-56633400	Enhancers	Colon Smooth Muscle	Colon
23	chr6:56628200-56631600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:56628200-56638400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:56628400-56629800	Enhancers	Psoas Muscle	Psoas
26	chr6:56628400-56633000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:56628400-56638400	Enhancers	Osteobl	bone
28	chr6:56628600-56630200	Enhancers	A549	lung
29	chr6:56628600-56631400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr6:56628600-56632000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr6:56628600-56632000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:56628600-56632000	Enhancers	Fetal Heart	heart
33	chr6:56628600-56633200	Enhancers	Brain Hippocampus Middle	brain
34	chr6:56628600-56634400	Enhancers	Brain Cingulate Gyrus	brain
35	chr6:56628600-56638200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:56628600-56638400	Enhancers	HSMM	muscle
37	chr6:56628800-56629800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:56628800-56632800	Enhancers	NHDF-Ad	bronchial
39	chr6:56629000-56630400	Enhancers	HUVEC	blood vessel
40	chr6:56629000-56631000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr6:56629000-56631800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr6:56629200-56630200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:56629200-56631000	Weak transcription	Hela-S3	cervix
44	chr6:56629200-56637600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:56629400-56629800	Enhancers	GM12878-XiMat	blood
46	chr6:56629400-56630400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:56629400-56630400	Weak transcription	Right Ventricle	heart
48	chr6:56629400-56630600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:56629400-56630600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:56629400-56630800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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