Variant report

Variant	rs11787602
Chromosome Location	chr9:116105712-116105713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr9:116105559-116106454	K562	blood:	n/a	n/a
2	GATA3	chr9:116105603-116106015	SH-SY5Y	brain:	n/a	n/a
3	KAP1	chr9:116105528-116105747	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116103587..116106029-chr9:116160047..116164950,6	MCF-7	breast:
2	chr9:116102720..116107904-chr9:116161009..116164019,5	MCF-7	breast:
3	chr9:116094633..116097880-chr9:116104158..116105941,3	MCF-7	breast:
4	chr9:116091449..116094429-chr9:116104938..116107109,2	MCF-7	breast:
5	chr9:116103857..116106255-chr9:116138187..116140554,2	MCF-7	breast:
6	chr9:116103291..116106183-chr9:116133139..116134993,2	K562	blood:
7	chr9:116063284..116065510-chr9:116102338..116105750,4	MCF-7	breast:

No data

Variant related genes	Relation type
WDR31	TF binding region
ENSG00000148218	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000165188	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10114327	0.89[ASN][1000 genomes]
rs10117906	0.85[ASN][1000 genomes]
rs10118045	0.85[ASN][1000 genomes]
rs10118275	0.85[ASN][1000 genomes]
rs10759640	0.91[ASN][1000 genomes]
rs10817481	0.88[ASN][1000 genomes]
rs10817483	0.93[AFR][1000 genomes]
rs10817485	0.85[ASN][1000 genomes]
rs10981730	0.81[AFR][1000 genomes]
rs10981734	0.82[ASN][1000 genomes]
rs10981735	0.81[AFR][1000 genomes]
rs10981762	0.85[ASN][1000 genomes]
rs10981763	0.84[ASN][1000 genomes]
rs10981764	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11788333	0.93[AFR][1000 genomes]
rs16932730	0.82[ASN][1000 genomes]
rs1998504	0.87[ASN][1000 genomes]
rs2093691	0.91[ASN][1000 genomes]
rs2296075	0.81[ASN][1000 genomes]
rs4979237	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4979238	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6478002	0.88[ASN][1000 genomes]
rs6478003	0.88[ASN][1000 genomes]
rs6478004	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478005	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478006	0.84[ASN][1000 genomes]
rs66790147	0.81[AFR][1000 genomes]
rs7025188	0.85[ASN][1000 genomes]
rs7025333	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7025371	0.86[ASN][1000 genomes]
rs7025517	0.82[ASN][1000 genomes]
rs7025770	0.84[ASN][1000 genomes]
rs7026076	0.85[ASN][1000 genomes]
rs7026114	0.81[AFR][1000 genomes]
rs7026831	0.81[AFR][1000 genomes]
rs7038589	0.81[AFR][1000 genomes]
rs7041572	0.87[ASN][1000 genomes]
rs7048039	0.88[ASN][1000 genomes]
rs7849513	0.87[ASN][1000 genomes]
rs7850002	0.90[ASN][1000 genomes]
rs7850003	0.83[ASN][1000 genomes]
rs7850264	0.86[ASN][1000 genomes]
rs7863921	0.91[ASN][1000 genomes]
rs7864788	0.87[ASN][1000 genomes]
rs7868271	0.90[ASN][1000 genomes]
rs7870848	0.88[AFR][1000 genomes]
rs912247	0.93[AFR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11787602	CDC26	cis	Thyroid	GTEx
rs11787602	BSPRY	cis	Heart Left Ventricle	GTEx
rs11787602	HDHD3	cis	Artery Tibial	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116102800-116105800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:116103000-116106200	Weak transcription	Esophagus	oesophagus
3	chr9:116103000-116107200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:116103000-116111800	Weak transcription	Lung	lung
5	chr9:116103200-116105800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:116103200-116105800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:116103200-116105800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:116103200-116105800	Weak transcription	Fetal Intestine Small	intestine
9	chr9:116103200-116105800	Weak transcription	Fetal Lung	lung
10	chr9:116103200-116105800	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:116103200-116105800	Weak transcription	NHDF-Ad	bronchial
12	chr9:116103200-116106000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:116103200-116106200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr9:116103200-116106200	Weak transcription	Colonic Mucosa	Colon
15	chr9:116103200-116106400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:116103200-116106400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:116103200-116107000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr9:116103200-116107200	Weak transcription	Brain Angular Gyrus	brain
19	chr9:116103200-116107400	Weak transcription	Fetal Intestine Large	intestine
20	chr9:116103200-116108000	Enhancers	Fetal Heart	heart
21	chr9:116103200-116108200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr9:116103200-116108600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:116103200-116108800	Weak transcription	Placenta	Placenta
24	chr9:116103200-116110000	Weak transcription	Right Atrium	heart
25	chr9:116103200-116111400	Weak transcription	Stomach Mucosa	stomach
26	chr9:116103200-116111400	Weak transcription	GM12878-XiMat	blood
27	chr9:116103400-116105800	Weak transcription	Liver	Liver
28	chr9:116103400-116105800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:116103400-116106200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:116103400-116106200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr9:116103400-116106200	Weak transcription	Pancreas	Pancrea
32	chr9:116103400-116106600	Weak transcription	Adipose Nuclei	Adipose
33	chr9:116103600-116106200	Weak transcription	Fetal Stomach	stomach
34	chr9:116104000-116106200	Weak transcription	Hela-S3	cervix
35	chr9:116104000-116108400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr9:116104600-116105800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:116104600-116105800	Weak transcription	K562	blood
38	chr9:116104600-116106400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:116104800-116106200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr9:116105000-116105800	Enhancers	Right Ventricle	heart
41	chr9:116105400-116108200	Enhancers	Brain Hippocampus Middle	brain
42	chr9:116105400-116108800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:116105600-116105800	Enhancers	Stomach Smooth Muscle	stomach
44	chr9:116105600-116106000	Enhancers	Brain Anterior Caudate	brain
45	chr9:116105600-116106600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:116105600-116106600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:116105600-116106600	Enhancers	Brain Cingulate Gyrus	brain
48	chr9:116105600-116106600	Enhancers	Left Ventricle	heart
49	chr9:116105600-116106600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr9:116105600-116106600	Enhancers	Dnd41	blood

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