Variant report

Variant	rs9647885
Chromosome Location	chr7:66768699-66768700
allele	G/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	HEY1	chr7:66768689-66768880	K562	blood:	n/a	n/a
2	POLR2A	chr7:66768589-66768903	GM12878	blood:	n/a	n/a
3	MXI1	chr7:66766533-66769081	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr7:66768678-66768878	GM12878	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
PMS2P4	TF binding region
STAG3L4	TF binding region
ENSG00000106610	Chromatin interaction
ENSG00000228019	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10245535	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1045513	0.82[AFR][1000 genomes]
rs10807709	0.82[AFR][1000 genomes]
rs11765520	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11766456	0.86[ASN][1000 genomes]
rs12533161	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13244247	0.82[AFR][1000 genomes]
rs2041575	0.82[AFR][1000 genomes]
rs2421299	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2421302	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28615085	0.82[AFR][1000 genomes]
rs35245276	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466388	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9647884	0.80[AFR][1000 genomes]
rs9647886	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv2156170	chr7:66768697-66768701	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9647885	STAG3L4	cis	Nerve Tibial	GTEx
rs9647885	TYW1	Cis_1M	lymphoblastoid	RTeQTL
rs9647885	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs9647885	STAG3L4	cis	Skin Sun Exposed Lower leg	GTEx
rs9647885	STAG3L4	cis	lung	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	chr7:66766200-66768800	Active TSS	Hela-S3	cervix
3	chr7:66766200-66769200	Active TSS	GM12878-XiMat	blood
4	chr7:66766400-66768800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:66766400-66769000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:66766400-66769000	Active TSS	A549	lung
7	chr7:66766600-66768800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr7:66766600-66768800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:66766600-66768800	Active TSS	Psoas Muscle	Psoas
10	chr7:66766600-66768800	Active TSS	Right Ventricle	heart
11	chr7:66766600-66768800	Active TSS	HepG2	liver
12	chr7:66766600-66768800	Active TSS	HSMMtube	muscle
13	chr7:66766600-66769000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr7:66766600-66769000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr7:66766600-66769000	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr7:66766600-66769000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:66766600-66769000	Active TSS	Fetal Kidney	kidney
18	chr7:66766600-66769200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:66766800-66768800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:66766800-66769000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:66766800-66769000	Active TSS	Muscle Satellite Cultured Cells	--
22	chr7:66766800-66769000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr7:66766800-66769200	Active TSS	HMEC	breast
24	chr7:66767000-66768800	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr7:66767000-66769000	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr7:66767400-66769000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:66767800-66780800	Weak transcription	Fetal Brain Male	brain
28	chr7:66768000-66768800	Active TSS	Right Atrium	heart
29	chr7:66768000-66769200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:66768000-66773600	Weak transcription	Stomach Mucosa	stomach
31	chr7:66768200-66769000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:66768200-66774000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr7:66768400-66768800	Weak transcription	Liver	Liver
34	chr7:66768400-66769000	Enhancers	Primary B cells from peripheral blood	blood
35	chr7:66768400-66769000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr7:66768400-66769200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr7:66768400-66769200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:66768400-66769400	Weak transcription	Primary T cells from cord blood	blood
39	chr7:66768400-66769800	Weak transcription	Pancreas	Pancrea
40	chr7:66768400-66770200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr7:66768400-66770200	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:66768400-66770200	Weak transcription	Fetal Heart	heart
43	chr7:66768400-66770400	Weak transcription	Lung	lung
44	chr7:66768400-66770400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:66768400-66770600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr7:66768400-66771200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:66768400-66771200	Weak transcription	Brain Substantia Nigra	brain
48	chr7:66768400-66771400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr7:66768400-66771800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:66768400-66772000	Weak transcription	Brain Germinal Matrix	brain

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