Variant report

Variant	rs2295924
Chromosome Location	chr9:101585831-101585832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101569167..101574169-chr9:101584327..101589428,7	K562	blood:
2	chr9:101568720..101574310-chr9:101584029..101588574,5	MCF-7	breast:
3	chr9:101559911..101562273-chr9:101583988..101585996,2	K562	blood:
4	chr9:101570303..101574512-chr9:101580563..101586059,9	K562	blood:
5	chr9:101583330..101586949-chr9:101590792..101593415,3	MCF-7	breast:
6	chr9:101579352..101582875-chr9:101585039..101587415,4	K562	blood:
7	chr9:101581569..101586454-chr9:101592165..101596926,7	K562	blood:

Variant related genes	Relation type
ENSG00000119514	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10987602	0.89[JPT][hapmap]
rs10987748	0.80[ASN][1000 genomes]
rs10987872	0.85[EUR][1000 genomes]
rs12341538	0.89[EUR][1000 genomes]
rs12686258	0.88[CHD][hapmap];0.89[JPT][hapmap]
rs2093503	0.88[EUR][1000 genomes]
rs2295925	0.85[ASW][hapmap];0.89[CEU][hapmap];0.82[LWK][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs3813711	0.91[EUR][1000 genomes]
rs4743284	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6478895	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7043234	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7861195	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs911928	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[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	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv973475	chr9:101579594-101593836	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv973474	chr9:101579594-101595565	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2295924	ANKS6	Cis_1M	lymphoblastoid	RTeQTL
rs2295924	GABBR2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101571000-101586600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:101572600-101586600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:101572800-101589200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:101573000-101586600	Weak transcription	Esophagus	oesophagus
5	chr9:101573000-101612800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:101573800-101586000	Weak transcription	Fetal Intestine Large	intestine
7	chr9:101576000-101605000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr9:101577800-101610600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:101578000-101596800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:101579200-101610800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:101581400-101586600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr9:101581400-101586600	Weak transcription	Colonic Mucosa	Colon
13	chr9:101581600-101586200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:101581600-101591000	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr9:101581800-101592400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:101582000-101588800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:101582000-101610600	Weak transcription	Aorta	Aorta
18	chr9:101583800-101588800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:101583800-101589600	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:101583800-101599600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:101583800-101610600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:101584400-101587200	Strong transcription	Fetal Intestine Small	intestine
23	chr9:101584400-101602000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:101584600-101586200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:101584800-101602600	Strong transcription	Fetal Stomach	stomach
26	chr9:101585000-101591000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr9:101585000-101610600	Weak transcription	Brain Angular Gyrus	brain
28	chr9:101585000-101611000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:101585200-101586000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr9:101585200-101586800	Enhancers	Stomach Mucosa	stomach
31	chr9:101585200-101589000	Weak transcription	Thymus	Thymus
32	chr9:101585200-101598800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr9:101585400-101586800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr9:101585400-101589200	Weak transcription	Pancreas	Pancrea
35	chr9:101585600-101586800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:101585600-101586800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:101585800-101586200	Weak transcription	K562	blood
38	chr9:101585800-101587000	Genic enhancers	Gastric	stomach
39	chr9:101585800-101587200	Strong transcription	Primary T cells from cord blood	blood
40	chr9:101585800-101587200	Strong transcription	Rectal Mucosa Donor 29	rectum

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