Variant report

Variant	rs9647886
Chromosome Location	chr7:66768879-66768880
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	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

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
ENSG00000106610	Chromatin interaction
ENSG00000228019	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1045513	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]
rs10807709	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13244247	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28615085	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57522994	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7791024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7804553	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7807630	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9647884	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9647885	0.82[AFR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9647886	FLJ13195	cis	lesional skin	skin_eQTL
rs9647886	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs9647886	ASL	cis	cerebellum	SCAN
rs9647886	STAG3L4	cis	Nerve Tibial	GTEx
rs9647886	STAG3L4	cis	Esophagus Mucosa	GTEx
rs9647886	STAG3L4	cis	Whole Blood	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	chr7:66766200-66769200	Active TSS	GM12878-XiMat	blood
3	chr7:66766400-66769000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:66766400-66769000	Active TSS	A549	lung
5	chr7:66766600-66769000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr7:66766600-66769000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr7:66766600-66769000	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr7:66766600-66769000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:66766600-66769000	Active TSS	Fetal Kidney	kidney
10	chr7:66766600-66769200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:66766800-66769000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:66766800-66769000	Active TSS	Muscle Satellite Cultured Cells	--
13	chr7:66766800-66769000	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr7:66766800-66769200	Active TSS	HMEC	breast
15	chr7:66767000-66769000	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr7:66767400-66769000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:66767800-66780800	Weak transcription	Fetal Brain Male	brain
18	chr7:66768000-66769200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:66768000-66773600	Weak transcription	Stomach Mucosa	stomach
20	chr7:66768200-66769000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:66768200-66774000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr7:66768400-66769000	Enhancers	Primary B cells from peripheral blood	blood
23	chr7:66768400-66769000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr7:66768400-66769200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr7:66768400-66769200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:66768400-66769400	Weak transcription	Primary T cells from cord blood	blood
27	chr7:66768400-66769800	Weak transcription	Pancreas	Pancrea
28	chr7:66768400-66770200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr7:66768400-66770200	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:66768400-66770200	Weak transcription	Fetal Heart	heart
31	chr7:66768400-66770400	Weak transcription	Lung	lung
32	chr7:66768400-66770400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:66768400-66770600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr7:66768400-66771200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:66768400-66771200	Weak transcription	Brain Substantia Nigra	brain
36	chr7:66768400-66771400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:66768400-66771800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:66768400-66772000	Weak transcription	Brain Germinal Matrix	brain
39	chr7:66768400-66772200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr7:66768400-66772200	Weak transcription	Spleen	Spleen
41	chr7:66768400-66772400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr7:66768400-66772400	Weak transcription	Brain Anterior Caudate	brain
43	chr7:66768400-66772400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr7:66768400-66772400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr7:66768400-66772600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:66768400-66772600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr7:66768400-66772600	Weak transcription	Aorta	Aorta
48	chr7:66768400-66772600	Weak transcription	Brain Angular Gyrus	brain
49	chr7:66768400-66772600	Weak transcription	Colonic Mucosa	Colon
50	chr7:66768400-66772600	Weak transcription	Fetal Lung	lung

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