Variant report

Variant	rs2093691
Chromosome Location	chr9:116107087-116107088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116102720..116107904-chr9:116161009..116164019,5	MCF-7	breast:
2	chr9:116106104..116109704-chr9:116111339..116114258,3	K562	blood:
3	chr9:116091449..116094429-chr9:116104938..116107109,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119411	Chromatin interaction
ENSG00000148218	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10114327	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10117906	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10118045	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10118275	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10124515	0.86[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs10759638	0.86[CHB][hapmap]
rs10759640	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759641	0.95[EUR][1000 genomes]
rs10817475	0.82[CHB][hapmap]
rs10817476	0.82[CHB][hapmap]
rs10817481	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817485	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981715	0.86[CHB][hapmap]
rs10981762	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981763	0.90[ASN][1000 genomes]
rs11787602	0.91[ASN][1000 genomes]
rs11789755	0.86[CHB][hapmap]
rs12343629	0.86[CHB][hapmap]
rs1323466	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1998504	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296073	0.85[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap]
rs3750532	0.85[CHB][hapmap]
rs3750533	0.86[CHB][hapmap]
rs3750534	0.86[CHB][hapmap]
rs3810921	0.82[CEU][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4979231	0.86[CHB][hapmap]
rs4979232	0.82[CHB][hapmap]
rs6478002	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6478003	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6478004	0.90[ASN][1000 genomes]
rs6478005	0.90[ASN][1000 genomes]
rs6478006	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7025188	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7025371	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7025517	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025770	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7026076	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027833	0.80[AFR][1000 genomes]
rs7041572	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7048039	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7849513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7850002	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7850264	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7860625	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7863921	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864788	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7868271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7873862	0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2093691	CDC26	cis	Esophagus Muscularis	GTEx
rs2093691	BSPRY	cis	Heart Left Ventricle	GTEx
rs2093691	IKBKAP	cis	parietal	SCAN
rs2093691	PRPF4	cis	Esophagus Muscularis	GTEx
rs2093691	CDC26	cis	Muscle Skeletal	GTEx
rs2093691	BSPRY	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116103000-116107200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:116103000-116111800	Weak transcription	Lung	lung
3	chr9:116103200-116107200	Weak transcription	Brain Angular Gyrus	brain
4	chr9:116103200-116107400	Weak transcription	Fetal Intestine Large	intestine
5	chr9:116103200-116108000	Enhancers	Fetal Heart	heart
6	chr9:116103200-116108200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr9:116103200-116108600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:116103200-116108800	Weak transcription	Placenta	Placenta
9	chr9:116103200-116110000	Weak transcription	Right Atrium	heart
10	chr9:116103200-116111400	Weak transcription	Stomach Mucosa	stomach
11	chr9:116103200-116111400	Weak transcription	GM12878-XiMat	blood
12	chr9:116104000-116108400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr9:116105400-116108200	Enhancers	Brain Hippocampus Middle	brain
14	chr9:116105400-116108800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:116105600-116107600	Enhancers	Colon Smooth Muscle	Colon
16	chr9:116105600-116107800	Enhancers	Primary hematopoietic stem cells	blood
17	chr9:116105600-116107800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr9:116105600-116107800	Enhancers	Rectal Smooth Muscle	rectum
19	chr9:116105600-116108200	Enhancers	Brain Substantia Nigra	brain
20	chr9:116105800-116107600	Enhancers	Fetal Lung	lung
21	chr9:116105800-116110200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr9:116105800-116111400	Enhancers	Fetal Intestine Small	intestine
23	chr9:116105800-116111400	Weak transcription	Right Ventricle	heart
24	chr9:116106000-116107200	Weak transcription	Brain Anterior Caudate	brain
25	chr9:116106000-116107200	Weak transcription	Small Intestine	intestine
26	chr9:116106200-116107600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:116106200-116111400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:116106400-116107400	Weak transcription	HepG2	liver
29	chr9:116106400-116108800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:116106400-116109200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:116106400-116110400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr9:116106600-116109400	Weak transcription	Colonic Mucosa	Colon
33	chr9:116106600-116110000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:116106600-116111400	Weak transcription	Liver	Liver
35	chr9:116106600-116111400	Weak transcription	Esophagus	oesophagus
36	chr9:116106600-116111400	Weak transcription	Pancreas	Pancrea
37	chr9:116106600-116111800	Weak transcription	K562	blood
38	chr9:116106800-116107200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr9:116107000-116108000	Enhancers	Duodenum Mucosa	Duodenum
40	chr9:116107000-116108200	Enhancers	Brain Cingulate Gyrus	brain
41	chr9:116107000-116108200	Enhancers	Rectal Mucosa Donor 29	rectum

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