Variant report

Variant	rs541568
Chromosome Location	chr9:971172-971173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:970488..973347-chr9:974585..976403,2	K562	blood:
2	chr9:962191..965396-chr9:970150..972525,3	MCF-7	breast:
3	chr9:959751..962676-chr9:970259..973174,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10816147	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10816155	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10977870	0.88[ASN][1000 genomes]
rs166789	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs279882	0.82[EUR][1000 genomes]
rs279886	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs279891	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs279911	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs417260	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742604	0.83[ASN][1000 genomes]
rs604973	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025492	chr9:478813-1157169	Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv539897	chr9:478813-1157169	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv429977	chr9:584087-983301	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv613037	chr9:643453-1138368	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv892000	chr9:678951-972476	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv817248	chr9:706283-1457665	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv831491	chr9:794113-974142	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv892010	chr9:841152-1069663	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1034070	chr9:911265-1152351	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	esv2755928	chr9:924525-985979	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv892013	chr9:943611-1047343	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1018926	chr9:965006-1014141	Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:969200-971800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
2	chr9:969400-971200	Bivalent Enhancer	Fetal Heart	heart
3	chr9:969400-971400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr9:969400-972000	Bivalent Enhancer	Left Ventricle	heart
5	chr9:969400-972200	Bivalent Enhancer	Spleen	Spleen
6	chr9:969400-973200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr9:969400-973400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr9:969600-971200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:969600-971200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:969600-971400	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr9:969600-971600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
12	chr9:969600-971600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:969600-971600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
14	chr9:969600-972000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:969600-972000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr9:969600-972000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:969600-972000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:969600-972000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr9:969600-973200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr9:969600-973400	Bivalent Enhancer	Lung	lung
21	chr9:969800-971400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
22	chr9:969800-971400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
23	chr9:969800-971600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr9:969800-971600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
25	chr9:969800-971600	Enhancers	Pancreas	Pancrea
26	chr9:969800-971800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
27	chr9:969800-971800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
28	chr9:969800-972000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr9:969800-972000	Bivalent Enhancer	Fetal Stomach	stomach
30	chr9:969800-972400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr9:969800-973200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr9:969800-973200	Bivalent Enhancer	Fetal Lung	lung
33	chr9:970200-971400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:970200-971400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
35	chr9:970200-971800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:970400-971400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:970600-973000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:970600-973000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr9:970800-971400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:970800-972000	Bivalent Enhancer	Fetal Intestine Large	intestine
41	chr9:970800-972400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr9:970800-972800	Bivalent/Poised TSS	Psoas Muscle	Psoas
43	chr9:971000-971400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr9:971000-971400	Bivalent Enhancer	Brain Germinal Matrix	brain
45	chr9:971000-971400	Enhancers	Right Ventricle	heart
46	chr9:971000-971600	Weak transcription	Gastric	stomach

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