Variant report

Variant	rs35642890
Chromosome Location	chr6:56674717-56674718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56674708..56676996-chr6:56685905..56688829,2	MCF-7	breast:
2	chr6:56673664..56675723-chr6:56706332..56709691,3	MCF-7	breast:
3	chr6:56674544..56676964-chr6:56706043..56709745,4	MCF-7	breast:
4	chr6:56667404..56671001-chr6:56671318..56674766,5	MCF-7	breast:
5	chr6:56672534..56675270-chr6:56701111..56703419,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000231441	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10498812	0.93[EUR][1000 genomes]
rs10498813	0.93[EUR][1000 genomes]
rs11756551	0.93[EUR][1000 genomes]
rs11970648	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13190854	0.92[EUR][1000 genomes]
rs13191826	0.85[AMR][1000 genomes]
rs13192540	0.89[EUR][1000 genomes]
rs13192931	0.89[EUR][1000 genomes]
rs13194625	0.93[EUR][1000 genomes]
rs13194904	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13195601	0.92[EUR][1000 genomes]
rs13198204	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13198597	0.85[EUR][1000 genomes]
rs13200166	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13200559	0.92[EUR][1000 genomes]
rs13200768	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13200868	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13201639	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13201733	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13203148	0.93[EUR][1000 genomes]
rs13203327	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13203681	0.89[EUR][1000 genomes]
rs13204466	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13205667	0.92[EUR][1000 genomes]
rs13207768	0.88[EUR][1000 genomes]
rs13208409	0.89[EUR][1000 genomes]
rs13211879	0.90[EUR][1000 genomes]
rs13214135	0.85[AMR][1000 genomes]
rs13214893	0.84[EUR][1000 genomes]
rs13215883	0.85[EUR][1000 genomes]
rs13218913	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13220618	0.93[EUR][1000 genomes]
rs13220628	0.93[EUR][1000 genomes]
rs13220851	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1610156	0.80[EUR][1000 genomes]
rs1610157	0.88[EUR][1000 genomes]
rs16888171	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888184	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16888186	0.83[EUR][1000 genomes]
rs17684730	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684748	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684772	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684784	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684802	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684878	0.89[EUR][1000 genomes]
rs17684884	0.89[EUR][1000 genomes]
rs17684941	0.85[EUR][1000 genomes]
rs17751966	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17751977	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17752002	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17752046	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17752106	0.89[EUR][1000 genomes]
rs17752213	0.84[EUR][1000 genomes]
rs1903332	0.85[EUR][1000 genomes]
rs28360570	0.85[EUR][1000 genomes]
rs34083827	0.83[EUR][1000 genomes]
rs34171958	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34228698	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34359353	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34425815	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34500949	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34520435	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34612783	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34614087	0.92[EUR][1000 genomes]
rs34640766	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34866877	0.92[EUR][1000 genomes]
rs34896026	0.92[EUR][1000 genomes]
rs34966024	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35073881	0.89[EUR][1000 genomes]
rs35080938	0.88[EUR][1000 genomes]
rs35081015	0.93[EUR][1000 genomes]
rs35225175	0.93[EUR][1000 genomes]
rs35242294	0.88[EUR][1000 genomes]
rs35251663	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35407078	0.92[EUR][1000 genomes]
rs35439100	0.92[EUR][1000 genomes]
rs35440408	0.83[EUR][1000 genomes]
rs35440822	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35461301	0.92[EUR][1000 genomes]
rs35566812	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35609883	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35696739	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35828379	0.88[EUR][1000 genomes]
rs35851452	0.92[EUR][1000 genomes]
rs35873865	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35886823	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35986172	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36022925	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36037734	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36094082	0.89[EUR][1000 genomes]
rs4299824	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4348308	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4371846	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4415160	0.91[EUR][1000 genomes]
rs4457154	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4532444	0.91[EUR][1000 genomes]
rs4587171	0.97[EUR][1000 genomes]
rs56037312	0.82[EUR][1000 genomes]
rs56368885	0.90[EUR][1000 genomes]
rs58980183	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59432342	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61601344	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62411366	0.89[EUR][1000 genomes]
rs62411367	0.92[EUR][1000 genomes]
rs62411372	0.95[EUR][1000 genomes]
rs62411375	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62411376	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6904535	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6905603	0.88[EUR][1000 genomes]
rs6910414	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6914293	0.88[EUR][1000 genomes]
rs6918949	0.88[EUR][1000 genomes]
rs6928104	0.89[EUR][1000 genomes]
rs6934714	0.91[EUR][1000 genomes]
rs71564854	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71564855	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71564856	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564861	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564863	0.89[EUR][1000 genomes]
rs7758867	0.91[EUR][1000 genomes]
rs7761501	0.89[EUR][1000 genomes]
rs7761729	0.88[EUR][1000 genomes]
rs7766565	0.83[EUR][1000 genomes]
rs7771085	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7775182	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1034418	chr6:56651245-56700449	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56668000-56679200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:56668800-56682600	Weak transcription	Aorta	Aorta
3	chr6:56671600-56675600	Enhancers	Placenta Amnion	Placenta Amnion
4	chr6:56671600-56679200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:56671800-56675600	Enhancers	Osteobl	bone
6	chr6:56672000-56679000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:56672600-56675600	Enhancers	Fetal Heart	heart
8	chr6:56672600-56679800	Weak transcription	Adipose Nuclei	Adipose
9	chr6:56672800-56675000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:56673000-56678400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:56673400-56675200	Enhancers	Psoas Muscle	Psoas
12	chr6:56673400-56675600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:56673600-56674800	Enhancers	NHDF-Ad	bronchial
14	chr6:56673600-56675000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:56673600-56675000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:56673600-56675600	Enhancers	HSMMtube	muscle
17	chr6:56674000-56676000	Enhancers	GM12878-XiMat	blood
18	chr6:56674000-56676200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:56674000-56677200	Weak transcription	Pancreas	Pancrea
20	chr6:56674000-56679000	Weak transcription	Brain Germinal Matrix	brain
21	chr6:56674000-56679200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:56674000-56679200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:56674000-56679200	Weak transcription	Brain Angular Gyrus	brain
24	chr6:56674000-56679200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:56674000-56680200	Weak transcription	Ovary	ovary
26	chr6:56674200-56675600	Enhancers	A549	lung
27	chr6:56674200-56675800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:56674200-56676000	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:56674200-56676200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr6:56674200-56678400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:56674200-56678600	Weak transcription	Brain Anterior Caudate	brain
32	chr6:56674200-56678600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr6:56674200-56678600	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:56674200-56679000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:56674200-56679000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:56674200-56679000	Weak transcription	NHLF	lung
37	chr6:56674200-56679200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:56674200-56679200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:56674200-56679200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:56674200-56679200	Weak transcription	Brain Substantia Nigra	brain
41	chr6:56674200-56679200	Weak transcription	Left Ventricle	heart
42	chr6:56674200-56679200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:56674200-56679200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:56674200-56682600	Weak transcription	Right Ventricle	heart
45	chr6:56674200-56692400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:56674200-56703000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:56674400-56674800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr6:56674400-56675600	Enhancers	HSMM	muscle
49	chr6:56674400-56678600	Weak transcription	NH-A	brain
50	chr6:56674400-56679200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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