Variant report

Variant	rs1045513
Chromosome Location	chr7:66774604-66774605
allele	C/G
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	chr7:66767822..66771270-chr7:66774228..66776532,3	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]
rs10807709	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13244247	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615085	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57522994	0.82[EUR][1000 genomes]
rs7791024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7804553	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7807630	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9647884	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9647885	0.82[AFR][1000 genomes]
rs9647886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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
rs1045513	STAG3L4	cis	Esophagus Mucosa	GTEx
rs1045513	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs1045513	STAG3L4	cis	Whole Blood	GTEx
rs1045513	STAG3L4	cis	Nerve Tibial	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	chr7:66768400-66776600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:66768600-66782400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:66768800-66775200	Strong transcription	Fetal Intestine Small	intestine
5	chr7:66768800-66783200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:66768800-66783400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:66769000-66774800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:66769000-66781200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:66769000-66785400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:66769200-66775200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:66769200-66776800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr7:66769400-66782800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:66769400-66783400	Strong transcription	Primary T cells from cord blood	blood
14	chr7:66769400-66785000	Strong transcription	Fetal Stomach	stomach
15	chr7:66769400-66785600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:66770000-66782800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:66770000-66783000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr7:66770000-66783400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr7:66770000-66785400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr7:66770200-66775200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:66770200-66780600	Strong transcription	Brain Hippocampus Middle	brain
22	chr7:66770200-66783400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:66770200-66785800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:66770400-66776200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:66770400-66783400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr7:66770400-66783400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:66770400-66783600	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:66770400-66786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:66770400-66786800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr7:66770600-66780400	Strong transcription	Fetal Thymus	thymus
31	chr7:66770600-66782800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr7:66770600-66785200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr7:66770600-66785400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:66770600-66786400	Weak transcription	Fetal Heart	heart
35	chr7:66770800-66774800	Strong transcription	Fetal Kidney	kidney
36	chr7:66770800-66776400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:66770800-66777000	Strong transcription	HSMM	muscle
38	chr7:66770800-66778400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:66770800-66780200	Strong transcription	HepG2	liver
40	chr7:66770800-66780400	Strong transcription	A549	lung
41	chr7:66770800-66783400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr7:66770800-66786800	Strong transcription	Liver	Liver
43	chr7:66771000-66785800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr7:66771200-66775200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr7:66771200-66776600	Strong transcription	Brain Substantia Nigra	brain
46	chr7:66771200-66781800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr7:66771200-66785000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:66771200-66785000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr7:66771400-66776400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:66771400-66778200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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