Variant report

Variant	rs10759636
Chromosome Location	chr9:116018777-116018778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115981374..115984099-chr9:116016863..116018969,2	MCF-7	breast:
2	chr9:116014996..116017587-chr9:116018102..116020800,2	K562	blood:
3	chr9:116016365..116018792-chr9:116102521..116104428,2	MCF-7	breast:
4	chr9:115985715..115987380-chr9:116017322..116019580,2	K562	blood:

Variant related genes	Relation type
ENSG00000148225	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000119321	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10123415	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10125992	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513189	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739388	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739390	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739392	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10759633	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10759637	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759638	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs10817461	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10817468	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981715	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs11789755	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs11792628	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12343629	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs2296073	0.82[CHB][hapmap]
rs3750532	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs3750533	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs3750534	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs4129395	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4129396	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4129397	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4284098	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4560868	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979226	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4979231	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs6477998	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6477999	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7022397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7038769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7041615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7850357	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7851395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7859354	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9299214	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv893746	chr9:115983540-116022826	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10759636	CDC26	cis	Muscle Skeletal	GTEx
rs10759636	ZNF618	cis	cerebellum	SCAN
rs10759636	CDC26	cis	Esophagus Muscularis	GTEx
rs10759636	CDC26	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115985000-116020800	Weak transcription	Aorta	Aorta
2	chr9:115985600-116020800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:115985800-116019000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:115985800-116021000	Weak transcription	Fetal Stomach	stomach
5	chr9:115987800-116021000	Weak transcription	Hela-S3	cervix
6	chr9:115989000-116019200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:115996000-116022200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr9:115996000-116031600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:115996200-116022400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr9:115996600-116019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:116004400-116020400	Weak transcription	Fetal Thymus	thymus
12	chr9:116006200-116020400	Weak transcription	Psoas Muscle	Psoas
13	chr9:116007200-116019200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr9:116007200-116019400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:116007200-116020800	Weak transcription	Ovary	ovary
16	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:116009600-116019000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:116009600-116020200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:116009600-116029800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr9:116010000-116020000	Weak transcription	GM12878-XiMat	blood
21	chr9:116010200-116031800	Weak transcription	Fetal Heart	heart
22	chr9:116011400-116020200	Weak transcription	A549	lung
23	chr9:116011400-116028800	Weak transcription	Fetal Kidney	kidney
24	chr9:116011600-116020600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr9:116011600-116021000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:116012200-116019400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:116012200-116019400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:116013400-116020200	Weak transcription	Fetal Intestine Large	intestine
29	chr9:116013400-116020600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:116013400-116020800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:116013400-116020800	Weak transcription	Small Intestine	intestine
32	chr9:116013400-116022200	Weak transcription	Gastric	stomach
33	chr9:116014200-116021000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr9:116014400-116019200	Weak transcription	Brain Hippocampus Middle	brain
35	chr9:116014400-116021000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr9:116014400-116022200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr9:116015000-116019800	Weak transcription	Placenta	Placenta
38	chr9:116015400-116020800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:116015400-116021000	Weak transcription	Thymus	Thymus
40	chr9:116016000-116020400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:116016000-116020800	Weak transcription	Brain Germinal Matrix	brain
42	chr9:116016200-116019000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:116016200-116019400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr9:116016200-116020000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:116016400-116020000	Weak transcription	Fetal Brain Male	brain
46	chr9:116016400-116021000	Weak transcription	Lung	lung
47	chr9:116016400-116022200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr9:116016800-116019400	Weak transcription	NHDF-Ad	bronchial
49	chr9:116016800-116020000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr9:116016800-116021000	Weak transcription	Pancreas	Pancrea

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