Variant report

Variant	rs12493291
Chromosome Location	chr3:42550651-42550652
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	chr3:42542738..42545212-chr3:42547259..42551511,4	MCF-7	breast:
2	chr3:42543515..42546582-chr3:42549981..42551633,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12493238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267535	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2284132	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]
rs406360	0.89[ASN][1000 genomes]
rs407931	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs414977	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs450812	0.91[ASN][1000 genomes]
rs735773	0.95[JPT][hapmap]
rs811198	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12493291	C3orf39	cis	parietal	SCAN
rs12493291	ZDHHC3	cis	parietal	SCAN
rs12493291	HHATL	cis	cerebellum	SCAN
rs12493291	VIPR1	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42544600-42551600	Weak transcription	Pancreas	Pancrea
2	chr3:42545400-42551400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr3:42545400-42553800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:42546600-42553800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:42547200-42561800	Genic enhancers	Fetal Intestine Small	intestine
6	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:42547800-42551000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:42548400-42551000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr3:42548400-42552400	Enhancers	Colonic Mucosa	Colon
10	chr3:42548600-42550800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:42548600-42550800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:42548600-42553000	Enhancers	Stomach Mucosa	stomach
13	chr3:42548800-42551600	Enhancers	Lung	lung
14	chr3:42548800-42553200	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr3:42549200-42551400	Weak transcription	Left Ventricle	heart
16	chr3:42549200-42551600	Weak transcription	Esophagus	oesophagus
17	chr3:42549200-42551600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:42549200-42561800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:42549400-42555800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:42549600-42550800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:42549800-42550800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr3:42549800-42551400	Weak transcription	Placenta	Placenta
23	chr3:42549800-42551600	Enhancers	Duodenum Mucosa	Duodenum
24	chr3:42549800-42552000	Enhancers	Small Intestine	intestine
25	chr3:42549800-42553000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:42549800-42553200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:42549800-42553200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:42549800-42557000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:42549800-42560600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:42550000-42556000	Weak transcription	Brain Anterior Caudate	brain
31	chr3:42550000-42560400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:42550200-42550800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr3:42550200-42551400	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr3:42550200-42553600	Genic enhancers	Primary T cells from cord blood	blood
35	chr3:42550200-42558200	Enhancers	Right Ventricle	heart
36	chr3:42550400-42550800	Enhancers	Fetal Intestine Large	intestine
37	chr3:42550400-42551200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:42550400-42551400	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr3:42550400-42551400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr3:42550400-42551600	Weak transcription	Fetal Heart	heart
41	chr3:42550400-42551600	Weak transcription	Gastric	stomach
42	chr3:42550400-42551800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:42550400-42555000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:42550400-42555600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:42550600-42550800	Bivalent/Poised TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:42550600-42550800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:42550600-42551200	Strong transcription	Spleen	Spleen
48	chr3:42550600-42555000	Enhancers	Adipose Nuclei	Adipose
49	chr3:42550600-42558800	Enhancers	Right Atrium	heart

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