Variant report

Variant	rs35494794
Chromosome Location	chr6:56580922-56580923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56579501..56581287-chr6:56582321..56583913,2	MCF-7	breast:
2	chr6:56578404..56582346-chr6:56590205..56594810,5	MCF-7	breast:
3	chr6:56580270..56582985-chr6:56587887..56589432,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10498811	0.85[EUR][1000 genomes]
rs10498812	0.83[AFR][1000 genomes]
rs11756551	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11961141	0.98[EUR][1000 genomes]
rs11961342	1.00[EUR][1000 genomes]
rs11968575	0.98[EUR][1000 genomes]
rs11970648	0.87[EUR][1000 genomes]
rs13191164	0.85[EUR][1000 genomes]
rs13192037	0.85[EUR][1000 genomes]
rs13192478	0.98[EUR][1000 genomes]
rs13192567	0.98[EUR][1000 genomes]
rs13194904	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13195601	0.83[AFR][1000 genomes]
rs13196211	0.83[EUR][1000 genomes]
rs13198399	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13198938	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13200559	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs13200768	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13200868	0.80[AMR][1000 genomes]
rs13203000	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13203148	0.83[AFR][1000 genomes]
rs13203327	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13204466	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13205013	0.85[EUR][1000 genomes]
rs13205667	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs13206849	0.85[EUR][1000 genomes]
rs13208409	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs13210876	0.97[EUR][1000 genomes]
rs13211879	0.83[AFR][1000 genomes]
rs13213878	0.97[EUR][1000 genomes]
rs13217390	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13219546	0.97[EUR][1000 genomes]
rs13219942	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16888118	0.85[EUR][1000 genomes]
rs16888124	0.85[EUR][1000 genomes]
rs16888126	0.82[EUR][1000 genomes]
rs16888128	0.86[EUR][1000 genomes]
rs16888130	0.86[EUR][1000 genomes]
rs16888133	0.85[EUR][1000 genomes]
rs16888135	0.97[EUR][1000 genomes]
rs17684511	0.85[EUR][1000 genomes]
rs17684553	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17684571	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17751682	0.85[EUR][1000 genomes]
rs17751695	0.85[EUR][1000 genomes]
rs2967960	0.97[EUR][1000 genomes]
rs2967963	0.96[EUR][1000 genomes]
rs3002003	0.97[EUR][1000 genomes]
rs3002004	0.97[EUR][1000 genomes]
rs3002006	0.97[EUR][1000 genomes]
rs3002007	0.96[EUR][1000 genomes]
rs3002008	0.97[EUR][1000 genomes]
rs3002009	0.97[EUR][1000 genomes]
rs3002010	0.97[EUR][1000 genomes]
rs3002011	0.97[EUR][1000 genomes]
rs34138864	0.85[EUR][1000 genomes]
rs34425815	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs34429594	0.99[EUR][1000 genomes]
rs34455199	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34463732	0.90[EUR][1000 genomes]
rs34465210	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34500949	0.80[AMR][1000 genomes]
rs34566275	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34576803	0.83[EUR][1000 genomes]
rs34587484	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34612783	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs34623351	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34703847	0.92[EUR][1000 genomes]
rs34724718	0.85[EUR][1000 genomes]
rs34803237	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34812826	0.98[EUR][1000 genomes]
rs34824960	0.98[EUR][1000 genomes]
rs34832779	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34866877	0.83[AFR][1000 genomes]
rs34966024	0.84[AMR][1000 genomes]
rs35206656	0.86[EUR][1000 genomes]
rs35225175	0.83[AFR][1000 genomes]
rs35326806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35407078	0.83[AFR][1000 genomes]
rs35408048	0.85[EUR][1000 genomes]
rs35439100	0.83[AFR][1000 genomes]
rs35619924	0.85[EUR][1000 genomes]
rs35637749	0.85[EUR][1000 genomes]
rs35668437	0.85[EUR][1000 genomes]
rs35687635	0.86[EUR][1000 genomes]
rs35696739	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs35828379	0.83[AFR][1000 genomes]
rs35873865	0.88[AMR][1000 genomes]
rs35876418	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35920751	0.98[EUR][1000 genomes]
rs35986172	0.84[AMR][1000 genomes]
rs36037734	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs36068365	1.00[EUR][1000 genomes]
rs4072271	0.86[EUR][1000 genomes]
rs4074101	0.85[EUR][1000 genomes]
rs4074102	0.85[EUR][1000 genomes]
rs4074103	0.82[EUR][1000 genomes]
rs41267675	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4275049	0.97[EUR][1000 genomes]
rs4457154	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4640889	0.97[EUR][1000 genomes]
rs5024547	0.85[EUR][1000 genomes]
rs55742092	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56101897	0.85[EUR][1000 genomes]
rs56368885	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59085778	0.98[EUR][1000 genomes]
rs59247267	0.97[EUR][1000 genomes]
rs60498201	0.97[EUR][1000 genomes]
rs62411366	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs62411367	0.93[AMR][1000 genomes]
rs62411372	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62412526	0.85[EUR][1000 genomes]
rs62412528	0.85[EUR][1000 genomes]
rs62412531	0.85[EUR][1000 genomes]
rs62412532	0.85[EUR][1000 genomes]
rs62412544	0.90[EUR][1000 genomes]
rs62412556	0.97[EUR][1000 genomes]
rs6901176	0.85[EUR][1000 genomes]
rs6924375	0.85[EUR][1000 genomes]
rs6926134	0.98[EUR][1000 genomes]
rs6928104	0.93[AMR][1000 genomes]
rs6938003	0.97[EUR][1000 genomes]
rs71564848	0.83[EUR][1000 genomes]
rs71564849	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71564854	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7767128	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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56570000-56585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:56570200-56590000	Weak transcription	Right Atrium	heart
3	chr6:56577200-56581200	Enhancers	HMEC	breast
4	chr6:56577200-56581400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:56577200-56581600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:56577600-56581000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:56577600-56581400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:56577600-56581400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:56577600-56583000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:56577800-56581000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:56577800-56581000	Enhancers	Liver	Liver
12	chr6:56577800-56581000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr6:56577800-56581200	Enhancers	Fetal Heart	heart
14	chr6:56577800-56581200	Enhancers	HepG2	liver
15	chr6:56577800-56581400	Enhancers	Brain Angular Gyrus	brain
16	chr6:56577800-56581400	Enhancers	Colon Smooth Muscle	Colon
17	chr6:56577800-56581400	Enhancers	Rectal Smooth Muscle	rectum
18	chr6:56577800-56581400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:56577800-56581600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:56577800-56581600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:56577800-56581600	Enhancers	Brain Anterior Caudate	brain
22	chr6:56577800-56581600	Enhancers	Brain Cingulate Gyrus	brain
23	chr6:56577800-56581600	Enhancers	Brain Hippocampus Middle	brain
24	chr6:56577800-56581600	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr6:56577800-56581600	Enhancers	Brain Substantia Nigra	brain
26	chr6:56577800-56581600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:56577800-56582600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:56577800-56582800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:56577800-56582800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:56577800-56583600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr6:56578000-56581600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr6:56578000-56581600	Enhancers	Psoas Muscle	Psoas
33	chr6:56578200-56581600	Enhancers	HSMM	muscle
34	chr6:56578400-56581200	Enhancers	GM12878-XiMat	blood
35	chr6:56578400-56581400	Enhancers	Hela-S3	cervix
36	chr6:56578400-56581600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:56578400-56583600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr6:56578600-56583000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr6:56579200-56581000	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr6:56579200-56581200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:56579200-56583400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:56579400-56581000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr6:56579400-56581000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr6:56579400-56581200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:56579400-56592000	Weak transcription	Lung	lung
46	chr6:56579600-56581600	Enhancers	NHLF	lung
47	chr6:56579800-56581000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:56580000-56581600	Enhancers	Fetal Brain Male	brain
49	chr6:56580200-56581000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:56580200-56581000	Enhancers	Fetal Stomach	stomach

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