Variant report

Variant	rs28615085
Chromosome Location	chr7:66769761-66769762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr7:66769757-66770086	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
STAG3L4	TF binding region
PMS2P4	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1045513	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10807709	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13244247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041575	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57522994	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7791024	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7804553	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7807630	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9647884	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9647885	0.82[AFR][1000 genomes]
rs9647886	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1032237	chr7:66644492-66785029	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1027702	chr7:66722103-66841913	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1031048	chr7:66722103-66844039	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	nsv970872	chr7:66742783-66776118	Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28615085	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs28615085	STAG3L4	cis	Nerve Tibial	GTEx
rs28615085	STAG3L4	cis	Whole Blood	GTEx
rs28615085	STAG3L4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66767800-66780800	Weak transcription	Fetal Brain Male	brain
2	chr7:66768000-66773600	Weak transcription	Stomach Mucosa	stomach
3	chr7:66768200-66774000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:66768400-66769800	Weak transcription	Pancreas	Pancrea
5	chr7:66768400-66770200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:66768400-66770200	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:66768400-66770200	Weak transcription	Fetal Heart	heart
8	chr7:66768400-66770400	Weak transcription	Lung	lung
9	chr7:66768400-66770400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr7:66768400-66770600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr7:66768400-66771200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:66768400-66771200	Weak transcription	Brain Substantia Nigra	brain
13	chr7:66768400-66771400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr7:66768400-66771800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:66768400-66772000	Weak transcription	Brain Germinal Matrix	brain
16	chr7:66768400-66772200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:66768400-66772200	Weak transcription	Spleen	Spleen
18	chr7:66768400-66772400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr7:66768400-66772400	Weak transcription	Brain Anterior Caudate	brain
20	chr7:66768400-66772400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:66768400-66772400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:66768400-66772600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:66768400-66772600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr7:66768400-66772600	Weak transcription	Aorta	Aorta
25	chr7:66768400-66772600	Weak transcription	Brain Angular Gyrus	brain
26	chr7:66768400-66772600	Weak transcription	Colonic Mucosa	Colon
27	chr7:66768400-66772600	Weak transcription	Fetal Lung	lung
28	chr7:66768400-66772600	Weak transcription	Gastric	stomach
29	chr7:66768400-66773200	Weak transcription	Fetal Brain Female	brain
30	chr7:66768400-66773200	Weak transcription	NHDF-Ad	bronchial
31	chr7:66768400-66773200	Weak transcription	Osteobl	bone
32	chr7:66768400-66773400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:66768400-66773400	Weak transcription	Ovary	ovary
34	chr7:66768400-66773400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr7:66768400-66773600	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:66768400-66773800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:66768400-66774000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:66768400-66774000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr7:66768400-66774600	Weak transcription	Small Intestine	intestine
40	chr7:66768400-66776600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr7:66768600-66769800	Weak transcription	Fetal Intestine Large	intestine
42	chr7:66768600-66770000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr7:66768600-66770000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr7:66768600-66770400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:66768600-66770400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr7:66768600-66771400	Weak transcription	Placenta	Placenta
47	chr7:66768600-66771600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:66768600-66771600	Weak transcription	Left Ventricle	heart
49	chr7:66768600-66772200	Weak transcription	Esophagus	oesophagus
50	chr7:66768600-66772200	Weak transcription	Thymus	Thymus

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