Variant report

Variant	rs41309243
Chromosome Location	chr9:86293838-86293839
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86293365..86298412-chr9:86320425..86323449,5	MCF-7	breast:
2	chr9:86291927..86294296-chr9:86299849..86302388,2	K562	blood:
3	chr9:86292466..86294297-chr9:86296270..86297964,2	K562	blood:
4	chr9:86290356..86292978-chr9:86293291..86295310,2	K562	blood:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10119441	0.93[ASN][1000 genomes]
rs10217326	0.93[ASN][1000 genomes]
rs1044214	0.85[ASN][1000 genomes]
rs10481737	0.93[ASN][1000 genomes]
rs1052690	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10868039	0.93[ASN][1000 genomes]
rs11140214	0.93[ASN][1000 genomes]
rs12346707	0.93[ASN][1000 genomes]
rs17421460	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2542804	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780971	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2780973	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2780976	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2780994	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781002	0.85[ASN][1000 genomes]
rs2781004	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2781005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2781006	0.85[ASN][1000 genomes]
rs2781007	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2811904	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2811910	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2811913	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2811914	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2811918	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs41308878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56403955	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6559740	0.93[ASN][1000 genomes]
rs72746868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746869	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746871	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746879	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9410882	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86252800-86294000	Weak transcription	Small Intestine	intestine
2	chr9:86260600-86300400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:86263400-86298800	Strong transcription	Fetal Thymus	thymus
4	chr9:86264600-86297000	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr9:86264800-86294600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:86264800-86295600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:86264800-86298200	Strong transcription	Dnd41	blood
8	chr9:86264800-86300200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:86265000-86295200	Strong transcription	HSMM	muscle
10	chr9:86265000-86296800	Strong transcription	Liver	Liver
11	chr9:86265000-86298800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr9:86266200-86296000	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:86266400-86298800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr9:86267400-86296800	Strong transcription	A549	lung
15	chr9:86267400-86297800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr9:86267600-86296800	Strong transcription	Primary hematopoietic stem cells	blood
17	chr9:86267800-86295400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr9:86268000-86295400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:86268000-86298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:86268200-86294800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr9:86269000-86294200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:86269200-86297800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:86269400-86298600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr9:86270400-86295400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:86270800-86298000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:86271200-86298000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:86272800-86294000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:86273600-86298600	Weak transcription	Stomach Mucosa	stomach
29	chr9:86273600-86299000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:86273800-86304000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:86276200-86295400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:86279800-86299200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr9:86280400-86307400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:86281600-86298800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr9:86282000-86298800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr9:86282000-86299000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr9:86282000-86300000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr9:86282400-86297000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr9:86282400-86298000	Strong transcription	Primary B cells from cord blood	blood
40	chr9:86282800-86296800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr9:86282800-86297800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr9:86283000-86297800	Strong transcription	Adipose Nuclei	Adipose
43	chr9:86283000-86298000	Strong transcription	HUVEC	blood vessel
44	chr9:86283000-86298200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr9:86283200-86297400	Strong transcription	Primary T cells from cord blood	blood
46	chr9:86283400-86295600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:86283400-86298000	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr9:86283400-86298000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:86283400-86299000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:86284000-86294800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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