Variant report

Variant	rs28360570
Chromosome Location	chr6:56717630-56717631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr6:56717328-56717713	T-47D	breast:	n/a	n/a
2	FOXA1	chr6:56717316-56717728	T-47D	breast:	n/a	n/a
3	RAD21	chr6:56715291-56717862	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56704167..56710132-chr6:56712428..56720773,11	MCF-7	breast:
2	chr6:56714424..56718313-chr6:56818301..56821248,4	MCF-7	breast:

Variant related genes	Relation type
DST	TF binding region
ENSG00000231441	Chromatin interaction
ENSG00000151917	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10498812	0.92[EUR][1000 genomes]
rs10498813	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11756551	0.82[EUR][1000 genomes]
rs13190854	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13192540	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13192931	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13194625	0.92[EUR][1000 genomes]
rs13194904	0.85[EUR][1000 genomes]
rs13195601	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13198204	0.85[EUR][1000 genomes]
rs13198597	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13200166	0.85[EUR][1000 genomes]
rs13200559	0.80[EUR][1000 genomes]
rs13200768	0.84[EUR][1000 genomes]
rs13201639	0.85[EUR][1000 genomes]
rs13201733	0.85[EUR][1000 genomes]
rs13203148	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13203327	0.81[EUR][1000 genomes]
rs13203681	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13204466	0.84[EUR][1000 genomes]
rs13205667	0.80[EUR][1000 genomes]
rs13207768	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13211879	0.90[EUR][1000 genomes]
rs13214893	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13215883	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13218913	0.85[EUR][1000 genomes]
rs13220618	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13220628	0.92[EUR][1000 genomes]
rs13220851	0.87[EUR][1000 genomes]
rs1610156	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1610157	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16888171	0.85[EUR][1000 genomes]
rs16888184	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16888186	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16888189	0.83[EUR][1000 genomes]
rs16888192	0.83[EUR][1000 genomes]
rs17684730	0.85[EUR][1000 genomes]
rs17684748	0.85[EUR][1000 genomes]
rs17684772	0.85[EUR][1000 genomes]
rs17684784	0.85[EUR][1000 genomes]
rs17684802	0.85[EUR][1000 genomes]
rs17684878	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17684884	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17684941	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17751966	0.85[EUR][1000 genomes]
rs17751977	0.85[EUR][1000 genomes]
rs17752002	0.85[EUR][1000 genomes]
rs17752046	0.85[EUR][1000 genomes]
rs17752106	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17752213	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1903332	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34083827	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34171958	0.86[EUR][1000 genomes]
rs34228698	0.85[EUR][1000 genomes]
rs34359353	0.86[EUR][1000 genomes]
rs34425815	0.85[EUR][1000 genomes]
rs34500949	0.80[EUR][1000 genomes]
rs34520435	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34612783	0.84[EUR][1000 genomes]
rs34614087	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34640766	0.85[EUR][1000 genomes]
rs34866877	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34896026	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35073881	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35080938	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35081015	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35225175	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35242294	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35251663	0.84[EUR][1000 genomes]
rs35407078	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35439100	0.93[EUR][1000 genomes]
rs35440408	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35440822	0.86[EUR][1000 genomes]
rs35461301	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35566812	0.83[EUR][1000 genomes]
rs35609883	0.85[EUR][1000 genomes]
rs35642890	0.85[EUR][1000 genomes]
rs35696739	0.85[EUR][1000 genomes]
rs35828379	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35851452	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35873865	0.83[EUR][1000 genomes]
rs35886823	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36022925	0.85[EUR][1000 genomes]
rs36037734	0.85[EUR][1000 genomes]
rs36094082	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4299824	0.85[EUR][1000 genomes]
rs4348308	0.85[EUR][1000 genomes]
rs4371846	0.85[EUR][1000 genomes]
rs4415160	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4457154	0.85[EUR][1000 genomes]
rs4532444	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4587171	0.83[EUR][1000 genomes]
rs56037312	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59432342	0.85[EUR][1000 genomes]
rs61601344	0.85[EUR][1000 genomes]
rs62411367	0.80[EUR][1000 genomes]
rs62411372	0.84[EUR][1000 genomes]
rs62411375	0.84[EUR][1000 genomes]
rs62411376	0.85[EUR][1000 genomes]
rs6904535	0.80[EUR][1000 genomes]
rs6905603	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6910414	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6914293	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6918949	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6934714	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71564854	0.85[EUR][1000 genomes]
rs71564855	0.86[EUR][1000 genomes]
rs71564856	0.85[EUR][1000 genomes]
rs71564861	0.85[EUR][1000 genomes]
rs71564863	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7758867	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7761501	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7761729	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7766565	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7771085	0.90[EUR][1000 genomes]
rs7775182	0.91[AMR][1000 genomes];0.93[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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56716400-56717800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:56716600-56717800	Enhancers	Placenta	Placenta
3	chr6:56716800-56717800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:56716800-56717800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:56716800-56718800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:56716800-56724600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:56716800-56727200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:56717000-56717800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:56717000-56717800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:56717000-56717800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:56717000-56717800	Enhancers	Fetal Kidney	kidney
12	chr6:56717000-56717800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:56717000-56718200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:56717000-56718600	Weak transcription	HepG2	liver
15	chr6:56717000-56720400	Weak transcription	Left Ventricle	heart
16	chr6:56717000-56727200	Weak transcription	Psoas Muscle	Psoas
17	chr6:56717200-56717800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr6:56717200-56717800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr6:56717200-56717800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:56717200-56717800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:56717200-56717800	Enhancers	Adipose Nuclei	Adipose
22	chr6:56717200-56717800	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr6:56717200-56717800	Enhancers	Brain Cingulate Gyrus	brain
24	chr6:56717200-56717800	Enhancers	Fetal Lung	lung
25	chr6:56717200-56717800	Enhancers	Fetal Muscle Leg	muscle
26	chr6:56717200-56717800	Enhancers	HSMMtube	muscle
27	chr6:56717200-56717800	Enhancers	Osteobl	bone
28	chr6:56717200-56718000	Enhancers	A549	lung
29	chr6:56717200-56718200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:56717200-56718400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:56717200-56718800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:56717200-56719600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:56717200-56720400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:56717200-56720400	Weak transcription	Right Atrium	heart
35	chr6:56717400-56717800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:56717400-56717800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:56717400-56717800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:56717400-56717800	Enhancers	Brain Substantia Nigra	brain
39	chr6:56717400-56717800	Enhancers	HUVEC	blood vessel
40	chr6:56717400-56717800	Enhancers	NHLF	lung
41	chr6:56717400-56718000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:56717400-56718200	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr6:56717400-56718800	Enhancers	H1 Cell Line	embryonic stem cell
44	chr6:56717400-56719800	Weak transcription	Right Ventricle	heart
45	chr6:56717400-56720000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr6:56717400-56720400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:56717400-56720400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr6:56717400-56720800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:56717400-56721000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:56717400-56721000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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