Variant report

Variant	rs28493578
Chromosome Location	chr12:123978292-123978293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123968718..123970630-chr12:123978290..123980538,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11497310	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11507743	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11516174	0.87[EUR][1000 genomes]
rs11516175	0.90[EUR][1000 genomes]
rs11516178	0.90[EUR][1000 genomes]
rs11522341	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11522342	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11522343	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11523309	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11535679	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs11572999	1.00[YRI][hapmap]
rs13303358	0.93[EUR][1000 genomes]
rs28703907	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28728075	0.91[CEU][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs28781570	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28894691	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61953496	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs786455	0.80[CEU][hapmap]
rs7957839	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9697330	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9697415	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9697423	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9723026	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9723244	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9777715	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9777830	0.93[AMR][1000 genomes];0.90[EUR][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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28493578	UNC119B	cis	cerebellum	SCAN
rs28493578	DDX55	cis	cerebellum	SCAN
rs28493578	TMED3	trans	parietal	SCAN
rs28493578	ANAPC5	cis	parietal	SCAN
rs28493578	TCTN2	cis	cerebellum	SCAN
rs28493578	DDX55	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123944600-123995600	Weak transcription	Hela-S3	cervix
2	chr12:123944600-124012200	Strong transcription	Fetal Stomach	stomach
3	chr12:123949000-123984400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:123950800-124007600	Weak transcription	Colonic Mucosa	Colon
5	chr12:123956800-123993400	Weak transcription	HMEC	breast
6	chr12:123956800-123995400	Weak transcription	Fetal Brain Male	brain
7	chr12:123957400-123982400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:123957400-123995400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:123957400-123995400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:123957600-123995400	Weak transcription	Pancreas	Pancrea
11	chr12:123957600-124003800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:123957800-123982600	Weak transcription	A549	lung
13	chr12:123960000-123995400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:123961600-123979200	Weak transcription	NHEK	skin
15	chr12:123961600-123995800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:123963000-123981200	Weak transcription	Esophagus	oesophagus
17	chr12:123964000-123978600	Weak transcription	Right Atrium	heart
18	chr12:123964200-123981200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:123964200-123981200	Weak transcription	Spleen	Spleen
20	chr12:123964200-123981400	Weak transcription	NHDF-Ad	bronchial
21	chr12:123964400-123981200	Weak transcription	Gastric	stomach
22	chr12:123965200-123981000	Weak transcription	Fetal Intestine Large	intestine
23	chr12:123965400-123981400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:123965400-123983000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:123965600-123979400	Weak transcription	HSMM	muscle
26	chr12:123965600-123981200	Weak transcription	NHLF	lung
27	chr12:123965600-123982600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:123966200-123978800	Weak transcription	Brain Angular Gyrus	brain
29	chr12:123968400-123978600	Weak transcription	Brain Substantia Nigra	brain
30	chr12:123968800-123978800	Weak transcription	Lung	lung
31	chr12:123968800-123981200	Weak transcription	Liver	Liver
32	chr12:123968800-123995400	Weak transcription	NH-A	brain
33	chr12:123969000-123979000	Weak transcription	Adipose Nuclei	Adipose
34	chr12:123969000-123993800	Weak transcription	HUVEC	blood vessel
35	chr12:123969400-123984600	Weak transcription	Thymus	Thymus
36	chr12:123969600-123979000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:123969800-123980800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:123969800-123982600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:123970000-123981000	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:123970000-124016400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:123970200-123978600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:123970400-123978600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:123970400-123979000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:123970400-123980600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:123970400-123980800	Weak transcription	Fetal Lung	lung
46	chr12:123970400-123980800	Weak transcription	Osteobl	bone
47	chr12:123970400-123981000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:123970600-123978800	Weak transcription	Ovary	ovary
49	chr12:123972400-123978800	Weak transcription	Fetal Intestine Small	intestine
50	chr12:123972400-123980800	Weak transcription	Fetal Kidney	kidney

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