Variant report

Variant	rs2398853
Chromosome Location	chr9:96399442-96399443
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	chr9:96397302..96399892-chr9:96415445..96418992,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10761251	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10761252	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10761254	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10761255	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821196	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992807	0.97[ASN][1000 genomes]
rs10992836	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992841	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992854	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1806458	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001994	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398851	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2398861	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3750358	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3750362	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763605	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743930	0.88[ASN][1000 genomes]
rs4744264	0.83[ASN][1000 genomes]
rs6479499	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479500	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479501	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7019745	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7024028	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028306	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][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	nsv893585	chr9:96363859-96403367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv1055035	chr9:96372269-96402747	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96374600-96399800	Weak transcription	K562	blood
2	chr9:96380200-96411800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:96380800-96399800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:96384600-96412200	Weak transcription	Stomach Mucosa	stomach
5	chr9:96387000-96411800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:96387200-96399800	Weak transcription	Fetal Heart	heart
7	chr9:96387600-96399600	Weak transcription	Fetal Kidney	kidney
8	chr9:96390200-96405400	Weak transcription	HepG2	liver
9	chr9:96390600-96399600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:96391400-96400800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr9:96391600-96399600	Strong transcription	Primary T cells from cord blood	blood
12	chr9:96391600-96399800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:96391600-96400200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:96391600-96400200	Strong transcription	Gastric	stomach
15	chr9:96391600-96402000	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:96391800-96400000	Strong transcription	Colonic Mucosa	Colon
17	chr9:96391800-96400400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr9:96391800-96400400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:96391800-96402400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:96391800-96402400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:96391800-96402400	Strong transcription	Placenta	Placenta
22	chr9:96392000-96399600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr9:96392000-96399800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:96392000-96400200	Strong transcription	Pancreas	Pancrea
25	chr9:96392000-96400400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr9:96392000-96403400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:96392200-96399800	Strong transcription	Adipose Nuclei	Adipose
28	chr9:96392200-96402200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr9:96392200-96402200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr9:96392200-96403800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr9:96392200-96412000	Weak transcription	HMEC	breast
32	chr9:96392200-96423600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr9:96392400-96399600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:96392400-96402600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr9:96392400-96402600	Strong transcription	Liver	Liver
36	chr9:96392600-96399600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:96392600-96399600	Weak transcription	Fetal Brain Male	brain
38	chr9:96392800-96399600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:96392800-96400000	Strong transcription	Fetal Lung	lung
40	chr9:96393200-96399800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr9:96393200-96402800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:96393600-96399800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:96393600-96399800	Weak transcription	HSMMtube	muscle
44	chr9:96393600-96400800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr9:96393600-96406600	Weak transcription	GM12878-XiMat	blood
46	chr9:96393800-96399800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:96393800-96399800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:96393800-96400200	Strong transcription	Spleen	Spleen
49	chr9:96394200-96400000	Strong transcription	Rectal Smooth Muscle	rectum
50	chr9:96395200-96400000	Strong transcription	NHLF	lung

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