Variant report

Variant	rs9647884
Chromosome Location	chr7:66768440-66768441
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	ZNF384	chr7:66767172-66768497	K562	blood:	n/a	n/a
2	MXI1	chr7:66766533-66769081	SK-N-SH	brain:	n/a	n/a
3	HEY1	chr7:66766986-66768450	K562	blood:	n/a	n/a

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

Variant related genes	Relation type
STAG3L4	TF binding region
PMS2P4	TF binding region
ENSG00000228019	Chromatin interaction
ENSG00000106610	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1045513	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10807709	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13244247	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2041575	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28615085	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57522994	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7791024	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7804553	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7807630	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9647885	0.80[AFR][1000 genomes]
rs9647886	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9647884	STAG3L4	cis	Nerve Tibial	GTEx
rs9647884	STAG3L4	cis	Esophagus Mucosa	GTEx
rs9647884	STAG3L4	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66765800-66769000	Active TSS	K562	blood
2	chr7:66766200-66768600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:66766200-66768800	Active TSS	Hela-S3	cervix
4	chr7:66766200-66769200	Active TSS	GM12878-XiMat	blood
5	chr7:66766400-66768600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:66766400-66768600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr7:66766400-66768600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:66766400-66768600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:66766400-66768600	Active TSS	HSMM	muscle
10	chr7:66766400-66768600	Active TSS	NHEK	skin
11	chr7:66766400-66768600	Active TSS	NHLF	lung
12	chr7:66766400-66768800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:66766400-66769000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:66766400-66769000	Active TSS	A549	lung
15	chr7:66766600-66768600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr7:66766600-66768600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr7:66766600-66768600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:66766600-66768600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr7:66766600-66768600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:66766600-66768600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr7:66766600-66768600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:66766600-66768600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:66766600-66768600	Active TSS	Esophagus	oesophagus
24	chr7:66766600-66768600	Active TSS	Fetal Intestine Small	intestine
25	chr7:66766600-66768600	Active TSS	Fetal Stomach	stomach
26	chr7:66766600-66768600	Active TSS	Left Ventricle	heart
27	chr7:66766600-66768800	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr7:66766600-66768800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:66766600-66768800	Active TSS	Psoas Muscle	Psoas
30	chr7:66766600-66768800	Active TSS	Right Ventricle	heart
31	chr7:66766600-66768800	Active TSS	HepG2	liver
32	chr7:66766600-66768800	Active TSS	HSMMtube	muscle
33	chr7:66766600-66769000	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr7:66766600-66769000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr7:66766600-66769000	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr7:66766600-66769000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:66766600-66769000	Active TSS	Fetal Kidney	kidney
38	chr7:66766600-66769200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:66766800-66768600	Active TSS	Fetal Intestine Large	intestine
40	chr7:66766800-66768600	Active TSS	Stomach Smooth Muscle	stomach
41	chr7:66766800-66768600	Active TSS	Thymus	Thymus
42	chr7:66766800-66768600	Active TSS	HUVEC	blood vessel
43	chr7:66766800-66768800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:66766800-66769000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:66766800-66769000	Active TSS	Muscle Satellite Cultured Cells	--
46	chr7:66766800-66769000	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr7:66766800-66769200	Active TSS	HMEC	breast
48	chr7:66767000-66768600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:66767000-66768600	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr7:66767000-66768600	Active TSS	Primary T helper cells PMA-I stimulated	--

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