Variant report

Variant	rs28815324
Chromosome Location	chr7:65565776-65565777
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65563235..65566518-chr7:65579011..65581335,3	MCF-7	breast:
2	chr7:65563649..65566683-chr7:65578224..65580127,3	MCF-7	breast:
3	chr7:65563372..65566895-chr7:65568965..65573405,4	MCF-7	breast:
4	chr7:65564438..65566579-chr7:65590943..65592744,2	MCF-7	breast:
5	chr7:65536863..65539073-chr7:65564586..65566634,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10950024	0.87[ASN][1000 genomes]
rs10950025	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10950027	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10950029	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11760805	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11767833	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12666485	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12671834	0.86[ASN][1000 genomes]
rs12673308	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs160641	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs160645	0.80[ASN][1000 genomes]
rs17138089	0.83[ASN][1000 genomes]
rs17138149	0.80[ASN][1000 genomes]
rs221986	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2451953	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2460427	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2465121	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs313817	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs313818	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs313823	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316305	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316306	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316316	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316320	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316323	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs316324	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316328	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs400767	0.82[ASN][1000 genomes]
rs4441996	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4718325	0.80[ASN][1000 genomes]
rs6460276	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6460281	0.82[ASN][1000 genomes]
rs67302640	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67397473	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs67688847	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6960870	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73136346	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73142233	0.81[ASN][1000 genomes]
rs73142245	0.80[ASN][1000 genomes]
rs73376394	0.86[ASN][1000 genomes]
rs73376401	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7782212	0.83[ASN][1000 genomes]
rs7787063	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs28815324	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs28815324	GS1-124K5.4	cis	Artery Aorta	GTEx
rs28815324	GS1-124K5.4	cis	Stomach	GTEx
rs28815324	GTF2IRD1P1	cis	Thyroid	GTEx
rs28815324	RNU6-96P	cis	Thyroid	GTEx
rs28815324	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs28815324	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs28815324	GS1-124K5.11	cis	Thyroid	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65558200-65569400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:65564400-65565800	Active TSS	Rectal Smooth Muscle	rectum
3	chr7:65564600-65565800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr7:65564600-65565800	Active TSS	Colon Smooth Muscle	Colon
5	chr7:65564600-65565800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
6	chr7:65564600-65565800	Active TSS	Fetal Brain Female	brain
7	chr7:65564600-65565800	Active TSS	Fetal Intestine Large	intestine
8	chr7:65564600-65565800	Flanking Active TSS	Placenta	Placenta
9	chr7:65564600-65565800	Active TSS	Ovary	ovary
10	chr7:65564600-65565800	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr7:65564600-65565800	Flanking Active TSS	Dnd41	blood
12	chr7:65564600-65566000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr7:65564600-65566000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:65564600-65566000	Active TSS	A549	lung
15	chr7:65564800-65565800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr7:65564800-65565800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr7:65564800-65565800	Active TSS	Placenta Amnion	Placenta Amnion
18	chr7:65565000-65565800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:65565000-65565800	Active TSS	Brain Hippocampus Middle	brain
20	chr7:65565000-65565800	Active TSS	Hela-S3	cervix
21	chr7:65565000-65566200	Active TSS	Duodenum Mucosa	Duodenum
22	chr7:65565200-65565800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:65565200-65565800	Active TSS	Primary T cells from cord blood	blood
24	chr7:65565200-65565800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:65565200-65565800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:65565200-65565800	Active TSS	Brain Germinal Matrix	brain
27	chr7:65565200-65565800	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr7:65565200-65565800	Active TSS	Stomach Mucosa	stomach
29	chr7:65565200-65565800	Active TSS	NHEK	skin
30	chr7:65565200-65566000	Active TSS	NHLF	lung
31	chr7:65565200-65579800	Weak transcription	Spleen	Spleen
32	chr7:65565400-65565800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:65565400-65565800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr7:65565400-65565800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:65565400-65565800	Enhancers	Fetal Thymus	thymus
36	chr7:65565400-65566000	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr7:65565400-65566000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr7:65565400-65566200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:65565400-65566200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr7:65565600-65565800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:65565600-65565800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:65565600-65565800	Enhancers	Primary hematopoietic stem cells	blood
43	chr7:65565600-65565800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr7:65565600-65565800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr7:65565600-65565800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:65565600-65565800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:65565600-65565800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:65565600-65565800	Enhancers	Adipose Nuclei	Adipose
49	chr7:65565600-65565800	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr7:65565600-65565800	Weak transcription	Colonic Mucosa	Colon

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