Variant report

Variant	rs12344626
Chromosome Location	chr9:97856467-97856468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97781725..97783265-chr9:97854758..97856539,2	MCF-7	breast:
2	chr9:97316263..97318654-chr9:97854756..97857107,2	MCF-7	breast:
3	chr9:97687308..97690068-chr9:97855270..97858001,3	MCF-7	breast:
4	chr9:97812899..97815881-chr9:97854427..97857279,2	MCF-7	breast:
5	chr9:97629078..97631329-chr9:97854502..97856532,2	MCF-7	breast:
6	chr9:97854621..97856479-chr9:97877579..97880119,2	MCF-7	breast:
7	chr9:97682387..97688736-chr9:97850073..97858737,16	MCF-7	breast:
8	chr9:97855830..97857854-chr9:97891574..97893753,2	MCF-7	breast:
9	chr9:97854598..97856829-chr9:97883315..97884818,2	MCF-7	breast:
10	chr9:97488631..97490154-chr9:97855041..97857989,2	MCF-7	breast:
11	chr9:97676581..97686973-chr9:97850461..97860722,21	MCF-7	breast:
12	chr9:97765900..97771029-chr9:97855530..97860219,8	MCF-7	breast:
13	chr9:97848613..97851879-chr9:97854740..97857228,3	K562	blood:
14	chr9:97777349..97778997-chr9:97854120..97856635,2	MCF-7	breast:
15	chr9:97389746..97395320-chr9:97854192..97858136,7	MCF-7	breast:
16	chr9:97564303..97567097-chr9:97855435..97857190,2	MCF-7	breast:
17	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231806	Chromatin interaction
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10283758	0.82[EUR][1000 genomes]
rs10993475	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10993479	0.84[EUR][1000 genomes]
rs10993483	0.84[EUR][1000 genomes]
rs12338907	0.82[EUR][1000 genomes]
rs12342782	0.82[EUR][1000 genomes]
rs12350646	0.82[EUR][1000 genomes]
rs12352586	0.82[EUR][1000 genomes]
rs12377946	0.84[EUR][1000 genomes]
rs17679141	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1889241	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28626189	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4237226	0.82[EUR][1000 genomes]
rs4647421	0.82[EUR][1000 genomes]
rs4647432	0.82[EUR][1000 genomes]
rs4647441	0.82[EUR][1000 genomes]
rs4743990	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4744443	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4744444	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4744445	0.82[EUR][1000 genomes]
rs62560523	0.81[EUR][1000 genomes]
rs879559	0.89[AFR][1000 genomes];0.86[EUR][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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr9:97846000-97861600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
8	chr9:97847600-97878400	Weak transcription	Dnd41	blood
9	chr9:97848800-97856800	Weak transcription	HUVEC	blood vessel
10	chr9:97849000-97858400	Enhancers	Brain Cingulate Gyrus	brain
11	chr9:97849200-97859200	Weak transcription	Fetal Brain Female	brain
12	chr9:97849200-97863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:97849800-97864600	Enhancers	Psoas Muscle	Psoas
14	chr9:97850000-97858200	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr9:97850000-97862000	Weak transcription	Hela-S3	cervix
16	chr9:97850800-97857400	Enhancers	Fetal Thymus	thymus
17	chr9:97851000-97857600	Enhancers	Brain Angular Gyrus	brain
18	chr9:97851400-97856600	Enhancers	Fetal Heart	heart
19	chr9:97851800-97856600	Enhancers	NH-A	brain
20	chr9:97851800-97856800	Enhancers	Esophagus	oesophagus
21	chr9:97851800-97858000	Enhancers	Brain Substantia Nigra	brain
22	chr9:97851800-97858600	Enhancers	Brain Hippocampus Middle	brain
23	chr9:97852000-97858000	Enhancers	Brain Anterior Caudate	brain
24	chr9:97852000-97858200	Enhancers	Right Atrium	heart
25	chr9:97852200-97857600	Enhancers	Adipose Nuclei	Adipose
26	chr9:97852400-97856600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr9:97852600-97856600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:97852600-97856600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr9:97852600-97856600	Enhancers	Left Ventricle	heart
30	chr9:97852600-97856800	Enhancers	Colon Smooth Muscle	Colon
31	chr9:97852600-97856800	Enhancers	Placenta	Placenta
32	chr9:97852600-97857600	Enhancers	Fetal Muscle Trunk	muscle
33	chr9:97852800-97856800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr9:97852800-97858000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:97853000-97856800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr9:97853200-97858000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr9:97853600-97856800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:97853800-97856600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr9:97853800-97860400	Weak transcription	Liver	Liver
40	chr9:97854000-97857200	Enhancers	HSMMtube	muscle
41	chr9:97854200-97857000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:97854200-97857000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr9:97854200-97862200	Weak transcription	Aorta	Aorta
44	chr9:97854200-97862200	Weak transcription	HepG2	liver
45	chr9:97854200-97862400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr9:97854400-97857000	Enhancers	Thymus	Thymus
47	chr9:97854600-97857000	Enhancers	Primary T cells from cord blood	blood
48	chr9:97854800-97856600	Weak transcription	Ovary	ovary
49	chr9:97854800-97860200	Genic enhancers	Stomach Smooth Muscle	stomach
50	chr9:97855000-97857800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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