Variant report

Variant	rs3750534
Chromosome Location	chr9:116060124-116060125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116058060..116060469-chr9:116158324..116161269,2	MCF-7	breast:
2	chr9:116036740..116039923-chr9:116057646..116061284,5	MCF-7	breast:
3	chr9:116060077..116063011-chr9:116109868..116112387,2	MCF-7	breast:
4	chr9:116060084..116062548-chr9:116172614..116174498,2	K562	blood:

Variant related genes	Relation type
ENSG00000136875	Chromatin interaction
ENSG00000119411	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000176386	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10117451	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10124515	0.81[CHB][hapmap]
rs10513189	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs10739390	0.87[CHB][hapmap]
rs10759636	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs10759637	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs10759638	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10817474	0.86[CEU][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10817475	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10981710	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981712	0.81[EUR][1000 genomes]
rs10981715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981720	0.81[EUR][1000 genomes]
rs10981762	0.81[CHB][hapmap]
rs11552582	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11789755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12236683	0.84[EUR][1000 genomes]
rs12343629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2093691	0.86[CHB][hapmap]
rs2296073	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3750532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750535	1.00[CEU][hapmap]
rs4560868	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs4979223	0.87[CHB][hapmap]
rs4979226	0.87[CHB][hapmap]
rs4979231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979232	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4979233	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6477998	0.87[CHB][hapmap]
rs6478000	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478006	0.81[CHB][hapmap]
rs7022397	0.86[CHB][hapmap]
rs7027833	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7041615	0.87[CHB][hapmap]
rs7847295	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7849326	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7849513	0.90[CHB][hapmap]
rs7850357	0.87[CHB][hapmap]
rs7851395	0.87[CHB][hapmap]
rs7860625	0.86[CHB][hapmap]
rs7868271	0.86[CHB][hapmap]
rs9299214	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap]

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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs3750534	CDC26	cis	parietal	SCAN
rs3750534	CDC26	cis	Heart Left Ventricle	GTEx
rs3750534	CDC26	cis	Artery Tibial	GTEx
rs3750534	CDC26	cis	Esophagus Muscularis	GTEx
rs3750534	PRPF4	cis	Thyroid	GTEx
rs3750534	CDC26	cis	Nerve Tibial	GTEx
rs3750534	CDC26	cis	Adipose Subcutaneous	GTEx
rs3750534	CDC26	cis	Muscle Skeletal	GTEx
rs3750534	CDC26	cis	Thyroid	GTEx
rs3750534	CDC26	cis	Esophagus Mucosa	GTEx
rs3750534	BSPRY	cis	Heart Left Ventricle	GTEx
rs3750534	CDC26	cis	Whole Blood	GTEx
rs3750534	CDC26	cis	Skin Sun Exposed Lower leg	GTEx
rs3750534	CDC26	cis	lung	GTEx
rs3750534	ZNF618	cis	cerebellum	SCAN
rs3750534	CDC26	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116050000-116062000	Weak transcription	Stomach Mucosa	stomach
2	chr9:116054200-116065000	Weak transcription	Fetal Kidney	kidney
3	chr9:116054600-116065200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:116054800-116060600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:116054800-116062200	Weak transcription	Colonic Mucosa	Colon
6	chr9:116054800-116062200	Weak transcription	Pancreas	Pancrea
7	chr9:116054800-116065200	Weak transcription	Esophagus	oesophagus
8	chr9:116055000-116060200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:116055000-116063800	Weak transcription	Spleen	Spleen
10	chr9:116055200-116085200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:116055600-116062200	Weak transcription	A549	lung
12	chr9:116055800-116061600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:116055800-116061800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:116055800-116062000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:116056000-116061000	Weak transcription	HSMM	muscle
16	chr9:116056000-116061200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:116056000-116062000	Weak transcription	Gastric	stomach
18	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
19	chr9:116056200-116060600	Weak transcription	Brain Germinal Matrix	brain
20	chr9:116056200-116061000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:116056200-116062200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:116056200-116062200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:116056200-116062200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr9:116056200-116062200	Weak transcription	HUVEC	blood vessel
25	chr9:116056200-116062600	Weak transcription	Primary B cells from cord blood	blood
26	chr9:116056400-116060200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:116056400-116061200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:116056400-116061400	Weak transcription	NH-A	brain
29	chr9:116056400-116061800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:116056400-116064600	Weak transcription	Fetal Intestine Large	intestine
31	chr9:116056600-116060200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:116056600-116062200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:116056600-116062200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr9:116056600-116062200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr9:116056600-116062400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr9:116056600-116065400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:116056800-116060200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:116056800-116061200	Weak transcription	Fetal Thymus	thymus
39	chr9:116056800-116062200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:116056800-116062200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr9:116056800-116062600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr9:116056800-116063200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr9:116056800-116065000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:116056800-116065200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:116057400-116062200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:116058200-116061600	Weak transcription	Fetal Intestine Small	intestine
47	chr9:116058400-116064600	Weak transcription	HepG2	liver
48	chr9:116058600-116060600	Enhancers	Placenta	Placenta
49	chr9:116059200-116062000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr9:116059600-116061000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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