Variant report

Variant	rs11072600
Chromosome Location	chr15:76867915-76867916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76855877..76857707-chr15:76866696..76869240,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1011083	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1011084	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10152247	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10851888	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10851889	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072602	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072607	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072610	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072612	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072616	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072618	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11629727	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11630402	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11631394	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11632670	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11632765	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11635273	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637096	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11852777	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11854850	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11855762	0.89[EUR][1000 genomes]
rs12437981	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12440511	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12440965	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12591622	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898810	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12904417	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910081	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910820	0.82[EUR][1000 genomes]
rs12914196	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1603860	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1809875	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2047504	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2120109	0.83[EUR][1000 genomes]
rs2164102	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2404604	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2404734	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2436996	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2454450	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2454451	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2454454	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2459361	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2461871	0.80[ASN][1000 genomes]
rs28895952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34103231	0.92[EUR][1000 genomes]
rs36114653	0.81[ASN][1000 genomes]
rs4886816	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886819	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56339024	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57682236	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62026889	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62026898	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7165053	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7181506	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8029283	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs965818	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1042514	chr15:76838221-76906382	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1038233	chr15:76855205-76895763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1037282	chr15:76859309-76895763	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1044453	chr15:76860198-76895763	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1620	chr15:76862152-76914288	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
16	nsv904402	chr15:76863023-76930805	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
17	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1042623	chr15:76863437-76999030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1039269	chr15:76863437-77057021	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11072600	SCAPER	cis	lung	GTEx
rs11072600	SCAPER	cis	Esophagus Mucosa	GTEx
rs11072600	SCAPER	cis	Whole Blood	GTEx
rs11072600	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs11072600	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs11072600	SCAPER	cis	Esophagus Muscularis	GTEx
rs11072600	ISL2	cis	Whole Blood	GTEx
rs11072600	SCAPER	cis	Artery Tibial	GTEx
rs11072600	SCAPER	cis	Adipose Subcutaneous	GTEx
rs11072600	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs11072600	SCAPER	cis	Stomach	GTEx
rs11072600	SCAPER	cis	Thyroid	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76846000-76869000	Weak transcription	Left Ventricle	heart
2	chr15:76846000-76869000	Weak transcription	Pancreas	Pancrea
3	chr15:76846200-76868800	Weak transcription	Fetal Intestine Small	intestine
4	chr15:76847000-76868200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr15:76850200-76868400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:76857000-76868800	Weak transcription	Liver	Liver
7	chr15:76858600-76869000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:76860000-76868400	Weak transcription	Esophagus	oesophagus
9	chr15:76861600-76869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr15:76861800-76869000	Weak transcription	Colonic Mucosa	Colon
11	chr15:76861800-76869000	Weak transcription	Placenta	Placenta
12	chr15:76862600-76868800	Weak transcription	Adipose Nuclei	Adipose
13	chr15:76862600-76869000	Weak transcription	Right Ventricle	heart
14	chr15:76862600-76872000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:76863000-76869000	Weak transcription	Fetal Muscle Leg	muscle
16	chr15:76863400-76868600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:76864000-76868000	Weak transcription	Primary B cells from cord blood	blood
18	chr15:76865000-76868800	Weak transcription	Osteobl	bone
19	chr15:76865000-76869000	Weak transcription	Gastric	stomach
20	chr15:76865000-76869000	Weak transcription	Psoas Muscle	Psoas
21	chr15:76865200-76868200	Weak transcription	Right Atrium	heart
22	chr15:76865200-76868800	Weak transcription	Primary T cells from cord blood	blood
23	chr15:76865200-76868800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:76865200-76869000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:76865200-76869000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:76865200-76869200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:76865200-76869200	Weak transcription	Fetal Stomach	stomach
28	chr15:76865400-76868400	Weak transcription	Ovary	ovary
29	chr15:76865400-76869000	Weak transcription	Fetal Lung	lung
30	chr15:76865600-76869000	Weak transcription	Brain Substantia Nigra	brain
31	chr15:76865600-76869000	Weak transcription	A549	lung
32	chr15:76865600-76869000	Weak transcription	HepG2	liver
33	chr15:76865600-76869400	Weak transcription	Brain Hippocampus Middle	brain
34	chr15:76867000-76868000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:76867000-76868200	Enhancers	Primary hematopoietic stem cells	blood
36	chr15:76867000-76868400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr15:76867000-76868400	Enhancers	Primary B cells from peripheral blood	blood
38	chr15:76867200-76868000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr15:76867400-76868800	Enhancers	Fetal Heart	heart
40	chr15:76867600-76868000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr15:76867600-76868000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:76867600-76868000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr15:76867600-76868800	Weak transcription	Small Intestine	intestine
44	chr15:76867600-76868800	Enhancers	Hela-S3	cervix
45	chr15:76867800-76868000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr15:76867800-76868000	Enhancers	GM12878-XiMat	blood
47	chr15:76867800-76868200	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr15:76867800-76868400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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