Variant report

Variant	rs3739752
Chromosome Location	chr9:98535187-98535188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98534328..98536116-chr9:98636365..98638226,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10124062	1.00[CEU][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28454319	0.81[AMR][1000 genomes]
rs4742751	0.81[CEU][hapmap]
rs4743320	0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs7031550	0.81[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap]
rs7042092	1.00[CEU][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7854146	0.87[MEX][hapmap]
rs7860168	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3739752	HEMGN	cis	parietal	SCAN
rs3739752	IARS	cis	cerebellum	SCAN
rs3739752	BARX1	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98531800-98535600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:98532200-98535400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:98532200-98535800	Enhancers	Fetal Intestine Small	intestine
4	chr9:98532600-98535200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:98532600-98535400	Enhancers	Pancreas	Pancrea
6	chr9:98532800-98535400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr9:98533000-98535400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:98533000-98535400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr9:98533000-98536000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:98533200-98535600	Enhancers	Fetal Intestine Large	intestine
11	chr9:98533400-98535600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr9:98533400-98535600	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr9:98533400-98535800	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr9:98533400-98536200	Enhancers	Fetal Stomach	stomach
15	chr9:98533600-98535200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr9:98533600-98535200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:98533600-98535400	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr9:98533800-98535200	Bivalent Enhancer	Fetal Brain Male	brain
19	chr9:98533800-98535400	Enhancers	Brain Angular Gyrus	brain
20	chr9:98533800-98535800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:98533800-98535800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:98533800-98535800	Enhancers	HSMM	muscle
23	chr9:98533800-98536000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr9:98534000-98535200	Bivalent Enhancer	Placenta	Placenta
25	chr9:98534000-98535200	Bivalent Enhancer	Fetal Thymus	thymus
26	chr9:98534000-98535400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr9:98534000-98535400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:98534000-98535400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr9:98534000-98535400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr9:98534000-98535400	Flanking Active TSS	Ovary	ovary
31	chr9:98534000-98535600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:98534200-98535400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:98534200-98535400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr9:98534200-98535400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr9:98534200-98535400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr9:98534200-98535800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr9:98534200-98536200	Enhancers	Fetal Lung	lung
38	chr9:98534200-98539800	Weak transcription	Lung	lung
39	chr9:98534400-98535200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:98534400-98535400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:98534400-98535400	Enhancers	Brain Anterior Caudate	brain
42	chr9:98534400-98535400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr9:98534400-98535600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr9:98534400-98535800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:98534600-98535200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:98534600-98535200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr9:98534800-98535200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr9:98534800-98535200	Active TSS	Rectal Smooth Muscle	rectum
49	chr9:98534800-98535200	Weak transcription	Right Atrium	heart
50	chr9:98534800-98535400	Enhancers	Duodenum Smooth Muscle	Duodenum

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