Variant report

Variant	rs10807709
Chromosome Location	chr7:66773109-66773110
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66767764..66769327-chr7:66772532..66774988,2	MCF-7	breast:
2	chr7:66766528..66769516-chr7:66770098..66773304,3	K562	blood:

Variant related genes	Relation type
ENSG00000106610	Chromatin interaction
ENSG00000067601	Chromatin interaction

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

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

rs_ID	r²[population]
rs1045513	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13244247	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2041575	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28615085	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57522994	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7791024	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7804553	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7807630	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9647884	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9647885	0.82[AFR][1000 genomes]
rs9647886	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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
rs10807709	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs10807709	STAG3L4	cis	Esophagus Mucosa	GTEx
rs10807709	STAG3L4	cis	Nerve Tibial	GTEx
rs10807709	STAG3L4	cis	Whole Blood	GTEx

Chromatin state (count:125 , 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	chr7:66768400-66773200	Weak transcription	Fetal Brain Female	brain
5	chr7:66768400-66773200	Weak transcription	NHDF-Ad	bronchial
6	chr7:66768400-66773200	Weak transcription	Osteobl	bone
7	chr7:66768400-66773400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:66768400-66773400	Weak transcription	Ovary	ovary
9	chr7:66768400-66773400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:66768400-66773600	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:66768400-66773800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:66768400-66774000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:66768400-66774000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:66768400-66774600	Weak transcription	Small Intestine	intestine
15	chr7:66768400-66776600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:66768600-66773400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:66768600-66774000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr7:66768600-66782400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:66768800-66773200	Weak transcription	Psoas Muscle	Psoas
20	chr7:66768800-66773200	Weak transcription	HSMMtube	muscle
21	chr7:66768800-66775200	Strong transcription	Fetal Intestine Small	intestine
22	chr7:66768800-66783200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr7:66768800-66783400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:66769000-66773200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:66769000-66773400	Weak transcription	HUVEC	blood vessel
26	chr7:66769000-66773400	Weak transcription	NH-A	brain
27	chr7:66769000-66773600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:66769000-66774800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:66769000-66781200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:66769000-66785400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:66769200-66773600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr7:66769200-66775200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:66769200-66776800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:66769400-66782800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr7:66769400-66783400	Strong transcription	Primary T cells from cord blood	blood
36	chr7:66769400-66785000	Strong transcription	Fetal Stomach	stomach
37	chr7:66769400-66785600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr7:66770000-66782800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:66770000-66783000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr7:66770000-66783400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr7:66770000-66785400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr7:66770200-66775200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:66770200-66780600	Strong transcription	Brain Hippocampus Middle	brain
44	chr7:66770200-66783400	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:66770200-66785800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr7:66770400-66776200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr7:66770400-66783400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr7:66770400-66783400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:66770400-66783600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr7:66770400-66786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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