Variant report

Variant	rs3757493
Chromosome Location	chr7:96656572-96656573
allele	A/C
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	RAD21	chr7:96655299-96657631	SK-N-SH	brain:	n/a	chr7:96655925-96655938 chr7:96657146-96657165
2	SUZ12	chr7:96655000-96657260	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAZ	chr7:96656523-96657379	IMR90	lung:	n/a	n/a
4	SMC3	chr7:96656317-96657484	SK-N-SH	brain:	n/a	chr7:96657150-96657164
5	CTCF	chr7:96656407-96657547	A549	lung:	n/a	chr7:96657143-96657164 chr7:96657149-96657165 chr7:96657438-96657447 chr7:96657148-96657166 chr7:96657340-96657353
6	SPI1	chr7:96656529-96657328	HL-60	blood:	n/a	chr7:96656698-96656705 chr7:96657095-96657108 chr7:96656632-96656645 chr7:96657097-96657106

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:96225537..96226097-chr7:96656475..96657185,2	MCF-7	breast:
2	chr7:95543308..95544949-chr7:96654875..96656626,2	MCF-7	breast:

Variant related genes	Relation type
DLX5	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11762454	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11772563	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11772600	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773615	0.80[ASN][1000 genomes]
rs13227082	0.84[ASN][1000 genomes]
rs13242759	0.80[ASN][1000 genomes]
rs1526087	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17658419	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34094002	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757492	0.88[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs6960249	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800583	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv824221	chr7:96620279-96669211	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3757493	ACN9	cis	parietal	SCAN
rs3757493	EMR2	trans	lymphoblastoid	seeQTL
rs3757493	ACN9	cis	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:96653200-96656600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr7:96654000-96657200	Bivalent Enhancer	Fetal Brain Male	brain
3	chr7:96654200-96656800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:96654400-96657200	Bivalent/Poised TSS	Fetal Brain Female	brain
5	chr7:96654600-96657000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:96654800-96656600	Weak transcription	Osteobl	bone
7	chr7:96655200-96656800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
8	chr7:96655200-96657200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
9	chr7:96655400-96656600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr7:96655400-96656600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
11	chr7:96655400-96656600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:96655400-96656600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:96655400-96656600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr7:96655400-96657200	Active TSS	Right Atrium	heart
15	chr7:96655600-96656600	Enhancers	Liver	Liver
16	chr7:96655600-96656600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr7:96655600-96656600	Weak transcription	Ovary	ovary
18	chr7:96655600-96656600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
19	chr7:96655600-96656600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
20	chr7:96655600-96656800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:96655600-96656800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr7:96655600-96656800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:96655600-96656800	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr7:96655600-96656800	Enhancers	Pancreas	Pancrea
25	chr7:96655600-96657000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:96655600-96657000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
27	chr7:96655600-96657200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr7:96655600-96657200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr7:96655600-96657200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:96655600-96657200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:96655600-96657200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
32	chr7:96655600-96657200	Enhancers	Spleen	Spleen
33	chr7:96655800-96656600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:96655800-96656600	Bivalent Enhancer	Fetal Stomach	stomach
35	chr7:96655800-96656600	Bivalent Enhancer	Left Ventricle	heart
36	chr7:96655800-96656600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
37	chr7:96655800-96657000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr7:96655800-96657000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
39	chr7:96655800-96657000	Bivalent Enhancer	Fetal Thymus	thymus
40	chr7:96655800-96657200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
41	chr7:96655800-96657200	Active TSS	Brain Anterior Caudate	brain
42	chr7:96655800-96657200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
43	chr7:96656000-96656600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
44	chr7:96656000-96656600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:96656000-96656600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
46	chr7:96656000-96656600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr7:96656000-96656600	Enhancers	Esophagus	oesophagus
48	chr7:96656000-96656600	Bivalent Enhancer	Fetal Lung	lung
49	chr7:96656000-96656800	Weak transcription	Gastric	stomach
50	chr7:96656000-96656800	Enhancers	Lung	lung

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