Variant report

Variant	rs28429270
Chromosome Location	chr9:98233509-98233510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98233432..98236653-chr9:98236835..98241063,4	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16909898	0.94[AFR][1000 genomes]
rs16909902	0.94[AFR][1000 genomes]
rs2282040	0.92[AFR][1000 genomes]
rs28390100	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28441412	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28448271	0.94[AFR][1000 genomes]
rs28474857	0.92[AFR][1000 genomes]
rs28601668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28673156	0.92[AFR][1000 genomes]
rs28676757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28698995	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
2	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
3	chr9:98225600-98234000	Weak transcription	Right Atrium	heart
4	chr9:98225800-98239600	Weak transcription	HMEC	breast
5	chr9:98225800-98239800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:98225800-98244000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
8	chr9:98226000-98251000	Weak transcription	Osteobl	bone
9	chr9:98226200-98238400	Weak transcription	NH-A	brain
10	chr9:98226200-98239000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr9:98226200-98239400	Weak transcription	NHEK	skin
12	chr9:98226200-98240800	Strong transcription	Fetal Intestine Large	intestine
13	chr9:98226200-98243400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr9:98226400-98234200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:98226400-98239200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:98226400-98239400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:98226400-98243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:98226400-98247800	Weak transcription	Stomach Mucosa	stomach
20	chr9:98226600-98239000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr9:98226600-98239200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:98226600-98239400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:98226600-98239600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr9:98226600-98239600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:98226600-98240000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr9:98226600-98240200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:98226800-98239400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:98227000-98242600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:98227000-98242800	Strong transcription	Fetal Muscle Leg	muscle
31	chr9:98227000-98243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:98227000-98243600	Strong transcription	Fetal Intestine Small	intestine
33	chr9:98227200-98239200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr9:98227200-98243000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr9:98227200-98243000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:98227200-98244800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:98227400-98239600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:98227400-98242000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:98227400-98242800	Strong transcription	Adipose Nuclei	Adipose
40	chr9:98227600-98248800	Weak transcription	Small Intestine	intestine
41	chr9:98227800-98243200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr9:98228000-98240400	Strong transcription	Left Ventricle	heart
43	chr9:98228000-98243400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:98228200-98238600	Strong transcription	Brain Substantia Nigra	brain
45	chr9:98228600-98239200	Strong transcription	Brain Hippocampus Middle	brain
46	chr9:98229000-98238800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr9:98229400-98237400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:98229600-98238200	Strong transcription	Brain Germinal Matrix	brain
49	chr9:98229800-98234800	Weak transcription	Spleen	Spleen
50	chr9:98229800-98246800	Weak transcription	Colon Smooth Muscle	Colon

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