Variant report

Variant	rs13208409
Chromosome Location	chr6:56628545-56628546
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56626571..56629083-chr6:56715214..56716823,2	MCF-7	breast:
2	chr6:56625069..56627235-chr6:56628459..56631328,2	K562	blood:
3	chr6:56622975..56624888-chr6:56627094..56628814,2	K562	blood:
4	chr6:56624772..56628939-chr6:56706585..56709491,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231441	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 152 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10498812	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10498813	0.85[EUR][1000 genomes]
rs11756551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11961141	0.81[EUR][1000 genomes]
rs11968575	0.81[EUR][1000 genomes]
rs11970648	0.92[EUR][1000 genomes]
rs13190854	0.84[EUR][1000 genomes]
rs13192478	0.81[EUR][1000 genomes]
rs13192540	0.81[EUR][1000 genomes]
rs13192567	0.81[EUR][1000 genomes]
rs13192931	0.81[EUR][1000 genomes]
rs13194625	0.85[EUR][1000 genomes]
rs13194904	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13195601	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13198204	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13198399	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13198938	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13200166	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13200559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13200768	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13200868	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13201639	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13201733	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13203000	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13203148	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13203327	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13203681	0.81[EUR][1000 genomes]
rs13204466	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13205667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13210876	0.82[EUR][1000 genomes]
rs13211879	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13213878	0.80[EUR][1000 genomes]
rs13214135	0.81[AMR][1000 genomes]
rs13217390	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13218913	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13219546	0.82[EUR][1000 genomes]
rs13219942	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs13220618	0.85[EUR][1000 genomes]
rs13220628	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13220851	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16888135	0.82[EUR][1000 genomes]
rs16888171	0.89[EUR][1000 genomes]
rs17684730	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17684748	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17684772	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17684784	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17684802	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17684878	0.81[EUR][1000 genomes]
rs17684884	0.81[EUR][1000 genomes]
rs17751966	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17751977	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17752002	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17752046	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17752106	0.81[EUR][1000 genomes]
rs2967960	0.81[EUR][1000 genomes]
rs2967963	0.80[EUR][1000 genomes]
rs3002003	0.82[EUR][1000 genomes]
rs3002004	0.82[EUR][1000 genomes]
rs3002006	0.82[EUR][1000 genomes]
rs3002007	0.83[EUR][1000 genomes]
rs3002008	0.82[EUR][1000 genomes]
rs3002009	0.82[EUR][1000 genomes]
rs3002010	0.82[EUR][1000 genomes]
rs3002011	0.82[EUR][1000 genomes]
rs34171958	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34228698	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34359353	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34425815	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34455199	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34465210	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34500949	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34520435	0.88[EUR][1000 genomes]
rs34566275	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34587484	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34612783	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34614087	0.84[EUR][1000 genomes]
rs34623351	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34640766	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34803237	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34812826	0.81[EUR][1000 genomes]
rs34824960	0.81[EUR][1000 genomes]
rs34832779	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34866877	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34896026	0.84[EUR][1000 genomes]
rs34966024	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35073881	0.81[EUR][1000 genomes]
rs35080938	0.80[EUR][1000 genomes]
rs35081015	0.85[EUR][1000 genomes]
rs35225175	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35251663	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35326806	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35407078	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35439100	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35440822	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35461301	0.84[EUR][1000 genomes]
rs35494794	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35566812	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35609883	0.89[EUR][1000 genomes]
rs35642890	0.89[EUR][1000 genomes]
rs35696739	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35828379	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35851452	0.84[EUR][1000 genomes]
rs35873865	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35876418	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35886823	0.87[EUR][1000 genomes]
rs35920751	0.81[EUR][1000 genomes]
rs35986172	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36022925	0.87[EUR][1000 genomes]
rs36037734	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36094082	0.81[EUR][1000 genomes]
rs41267675	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4275049	0.82[EUR][1000 genomes]
rs4299824	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4348308	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4371846	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4415160	0.83[EUR][1000 genomes]
rs4457154	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4532444	0.85[EUR][1000 genomes]
rs4587171	0.86[EUR][1000 genomes]
rs4640889	0.82[EUR][1000 genomes]
rs56368885	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58980183	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59085778	0.81[EUR][1000 genomes]
rs59247267	0.82[EUR][1000 genomes]
rs59432342	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60498201	0.80[EUR][1000 genomes]
rs61601344	0.92[EUR][1000 genomes]
rs62411366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62411367	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62411372	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62411375	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62411376	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62412556	0.80[EUR][1000 genomes]
rs6904535	0.97[EUR][1000 genomes]
rs6926134	0.81[EUR][1000 genomes]
rs6928104	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6934714	0.83[EUR][1000 genomes]
rs6938003	0.81[EUR][1000 genomes]
rs71564854	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71564855	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71564856	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71564861	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71564863	0.81[EUR][1000 genomes]
rs7758867	0.83[EUR][1000 genomes]
rs7761501	0.81[EUR][1000 genomes]
rs7771085	0.86[EUR][1000 genomes]
rs7775182	0.84[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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56619800-56629200	Weak transcription	Pancreas	Pancrea
2	chr6:56621400-56629000	Weak transcription	Aorta	Aorta
3	chr6:56621400-56634200	Weak transcription	Spleen	Spleen
4	chr6:56622400-56637600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:56622800-56628800	Weak transcription	Ovary	ovary
6	chr6:56622800-56631000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:56623000-56631000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:56623200-56628800	Weak transcription	HepG2	liver
9	chr6:56623200-56629000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr6:56623200-56629000	Weak transcription	HUVEC	blood vessel
11	chr6:56623200-56629200	Weak transcription	Stomach Mucosa	stomach
12	chr6:56623200-56631000	Weak transcription	Fetal Lung	lung
13	chr6:56623400-56628600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:56623600-56628600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:56623600-56631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:56623600-56637200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:56623600-56637600	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:56623800-56628600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:56623800-56628800	Weak transcription	Lung	lung
20	chr6:56623800-56628800	Weak transcription	NH-A	brain
21	chr6:56623800-56630200	Weak transcription	HSMMtube	muscle
22	chr6:56623800-56630400	Weak transcription	Fetal Stomach	stomach
23	chr6:56624000-56628600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:56624000-56628600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:56624200-56628800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:56624200-56628800	Weak transcription	Fetal Thymus	thymus
27	chr6:56624600-56628600	Weak transcription	NHLF	lung
28	chr6:56624800-56628600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:56624800-56628600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:56624800-56628800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:56624800-56628800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:56624800-56628800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:56624800-56628800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:56624800-56629000	Weak transcription	Brain Angular Gyrus	brain
35	chr6:56624800-56629000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:56625000-56628600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:56625200-56628600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:56625200-56637800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:56625400-56629000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:56625400-56629000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:56625400-56631400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:56625600-56628800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:56625600-56637000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr6:56625600-56649800	Weak transcription	Brain Germinal Matrix	brain
45	chr6:56625800-56628800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:56625800-56637000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr6:56626000-56628600	Weak transcription	Brain Hippocampus Middle	brain
48	chr6:56626000-56628600	Weak transcription	Brain Substantia Nigra	brain
49	chr6:56626000-56628800	Weak transcription	Brain Anterior Caudate	brain
50	chr6:56626200-56628800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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