Variant report

Variant	rs28874007
Chromosome Location	chr5:74778669-74778670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74770863..74773429-chr5:74777117..74779848,3	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10036682	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10038945	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10041470	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10055011	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059022	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10061689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067900	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10074747	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10076819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077427	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10078671	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10474437	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12173076	0.88[EUR][1000 genomes]
rs13360099	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361353	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1469051	0.90[EUR][1000 genomes]
rs1553234	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1820049	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1909719	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287710	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28408106	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28612248	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668361	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3804231	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703671	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4703675	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4704213	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4704229	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56859362	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5744544	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744545	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744636	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5744667	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5744704	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5744709	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5744712	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57907925	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58519566	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58841453	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6891560	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633963	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72633964	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72633965	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72633966	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72633967	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633968	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72633969	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633970	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633971	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633972	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72633973	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72633974	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72633975	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633976	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633977	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7356633	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7726478	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs904743	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9293652	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9293654	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9293655	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs979182	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription 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	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 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	chr5:74732000-74787400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:74742400-74794200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:74760400-74792200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:74762200-74805800	Weak transcription	Pancreas	Pancrea
5	chr5:74763200-74787400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:74764800-74785800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:74764800-74786200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:74764800-74798600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:74765200-74795400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:74765200-74804600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:74765800-74786800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:74765800-74787200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:74766200-74785600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:74766600-74785600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:74767000-74779400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:74767400-74787000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:74769200-74794000	Weak transcription	Fetal Thymus	thymus
18	chr5:74769400-74779800	Weak transcription	Fetal Intestine Large	intestine
19	chr5:74769400-74794800	Weak transcription	Stomach Mucosa	stomach
20	chr5:74770400-74805200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:74771400-74785600	Weak transcription	Liver	Liver
22	chr5:74771800-74794200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:74772800-74779800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr5:74773200-74787800	Weak transcription	Ovary	ovary
25	chr5:74774800-74780400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr5:74775000-74785800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr5:74775200-74804000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:74775400-74780000	Strong transcription	Primary B cells from cord blood	blood
29	chr5:74776200-74778800	ZNF genes & repeats	GM12878-XiMat	blood
30	chr5:74776600-74778800	Enhancers	Psoas Muscle	Psoas
31	chr5:74777000-74779200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:74777000-74785800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr5:74777000-74787000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:74777000-74794200	Weak transcription	Dnd41	blood
35	chr5:74777200-74785800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:74777200-74787400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:74777400-74778800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:74777400-74797800	Weak transcription	Colonic Mucosa	Colon
39	chr5:74777800-74778800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:74778000-74778800	Enhancers	Aorta	Aorta
41	chr5:74778000-74778800	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr5:74778000-74779600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr5:74778200-74779000	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr5:74778200-74779000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr5:74778400-74779400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
46	chr5:74778400-74779800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:74778600-74780800	Weak transcription	Fetal Intestine Small	intestine
48	chr5:74778600-74785800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr5:74778600-74785800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:74778600-74785800	Weak transcription	Left Ventricle	heart

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