Variant report

Variant	rs28528275
Chromosome Location	chr7:21472265-21472266
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:21465891..21468738-chr7:21469069..21472897,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105866	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10046561	1.00[EUR][1000 genomes]
rs10216269	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10228982	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10232146	1.00[EUR][1000 genomes]
rs10233925	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10234687	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10235230	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10238881	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10250403	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10250517	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10252594	1.00[EUR][1000 genomes]
rs10254442	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10254858	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10255890	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10258911	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10259756	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10265366	1.00[EUR][1000 genomes]
rs10268107	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10274755	0.85[AFR][1000 genomes]
rs10275955	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10279096	1.00[EUR][1000 genomes]
rs10282629	1.00[EUR][1000 genomes]
rs12674126	1.00[AMR][1000 genomes]
rs2158415	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2285941	1.00[AMR][1000 genomes]
rs28419471	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28439880	1.00[EUR][1000 genomes]
rs28490171	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28580454	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28646037	1.00[EUR][1000 genomes]
rs28657649	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28661383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28666837	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55645999	1.00[EUR][1000 genomes]
rs55840028	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55879742	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55908918	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57142662	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57213984	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58025439	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58223300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61043546	0.86[AFR][1000 genomes]
rs6946711	0.85[AFR][1000 genomes]
rs6947378	0.85[AFR][1000 genomes]
rs6953601	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6972886	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6973902	1.00[AMR][1000 genomes]
rs73682368	1.00[EUR][1000 genomes]
rs73682608	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73685128	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73685129	1.00[EUR][1000 genomes]
rs73685130	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73685131	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73685134	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73685135	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73685138	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73685141	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73685144	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73685152	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73685154	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7792713	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027302	chr7:21391598-21727016	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv538800	chr7:21391598-21727016	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1028434	chr7:21468437-21636671	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21468400-21490600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:21468400-21497800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:21468600-21476600	Weak transcription	NHEK	skin
4	chr7:21468600-21478800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:21468600-21488600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr7:21468600-21495600	Weak transcription	Fetal Intestine Large	intestine
7	chr7:21468800-21489000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:21468800-21493600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:21469000-21474800	Weak transcription	A549	lung
10	chr7:21469000-21483800	Weak transcription	Adipose Nuclei	Adipose
11	chr7:21469800-21474400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:21470000-21472400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr7:21470000-21488600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:21470000-21490400	Weak transcription	Fetal Kidney	kidney
15	chr7:21470000-21497800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:21470200-21488600	Weak transcription	Gastric	stomach
17	chr7:21470200-21490600	Weak transcription	Psoas Muscle	Psoas
18	chr7:21470200-21494400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:21470400-21472400	Weak transcription	Lung	lung
20	chr7:21470400-21472400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:21470400-21472400	Active TSS	GM12878-XiMat	blood
22	chr7:21470400-21472800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:21470400-21477400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:21470400-21481000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:21470400-21488600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:21470400-21490600	Weak transcription	Pancreas	Pancrea
27	chr7:21470400-21494600	Weak transcription	Fetal Stomach	stomach
28	chr7:21470400-21516600	Weak transcription	Liver	Liver
29	chr7:21470400-21536400	Weak transcription	Esophagus	oesophagus
30	chr7:21470600-21472400	Weak transcription	Right Ventricle	heart
31	chr7:21470600-21472400	Active TSS	Thymus	Thymus
32	chr7:21470600-21472800	Active TSS	Fetal Brain Female	brain
33	chr7:21470600-21475200	Weak transcription	Fetal Muscle Leg	muscle
34	chr7:21470600-21477400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr7:21470600-21490800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr7:21470800-21472400	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr7:21470800-21472600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr7:21471000-21472800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr7:21471400-21472800	Enhancers	Colon Smooth Muscle	Colon
40	chr7:21471400-21473200	Enhancers	Primary B cells from peripheral blood	blood
41	chr7:21471400-21480200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr7:21471600-21472400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr7:21471600-21472400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr7:21471600-21473000	Enhancers	Brain Substantia Nigra	brain
45	chr7:21471600-21473200	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr7:21471600-21474800	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr7:21471600-21488400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:21471800-21472400	Weak transcription	Fetal Thymus	thymus
49	chr7:21471800-21472600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:21471800-21472800	Enhancers	Cortex derived primary cultured neurospheres	brain

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