Variant report

Variant	rs28413969
Chromosome Location	chr12:123946499-123946500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr12:123945849-123946856	SK-N-SH	brain:	n/a	chr12:123946654-123946664
2	MXI1	chr12:123945649-123946767	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123849466..123851432-chr12:123945194..123947485,2	MCF-7	breast:
2	chr12:123941363..123944201-chr12:123944495..123947371,3	MCF-7	breast:
3	chr12:123945278..123947489-chr12:123951548..123953733,2	K562	blood:
4	chr12:123944654..123946936-chr12:123957621..123961049,4	K562	blood:
5	chr12:123945506..123947749-chr12:123948281..123950619,2	K562	blood:
6	chr12:123946001..123947583-chr12:124097381..124100136,2	K562	blood:
7	chr12:123941560..123944210-chr12:123946389..123948077,2	K562	blood:

No data

Variant related genes	Relation type
SNRNP35	TF binding region
ENSG00000256092	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000111364	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11507739	0.91[EUR][1000 genomes]
rs11507740	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13303080	0.89[EUR][1000 genomes]
rs13303107	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13303167	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13303200	0.89[EUR][1000 genomes]
rs13303266	0.94[EUR][1000 genomes]
rs28483351	0.89[EUR][1000 genomes]
rs28497891	0.88[EUR][1000 genomes]
rs28557411	0.87[EUR][1000 genomes]
rs28667043	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34047494	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34351395	0.89[EUR][1000 genomes]
rs34762274	0.89[EUR][1000 genomes]
rs35090528	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35157218	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35370271	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35970945	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36084544	0.88[EUR][1000 genomes]
rs4047517	0.94[EUR][1000 genomes]
rs56412477	0.95[EUR][1000 genomes]
rs56860279	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6606748	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71456799	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7297035	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7300562	0.93[EUR][1000 genomes]
rs7306670	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7315901	0.96[EUR][1000 genomes]
rs7960816	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7975122	0.97[EUR][1000 genomes]
rs7978323	0.96[EUR][1000 genomes]
rs9330649	0.85[EUR][1000 genomes]
rs9697459	0.87[EUR][1000 genomes]
rs9697581	0.89[EUR][1000 genomes]
rs9697628	0.87[EUR][1000 genomes]
rs9697735	0.87[EUR][1000 genomes]
rs9777736	0.81[EUR][1000 genomes]
rs9778001	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9803116	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123943600-123949200	Weak transcription	Ovary	ovary
2	chr12:123943600-123955800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123943800-123947400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:123943800-123947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:123943800-123947600	Weak transcription	Liver	Liver
6	chr12:123943800-123947800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:123943800-123949000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:123943800-123949000	Weak transcription	Osteobl	bone
9	chr12:123943800-123949200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:123943800-123949200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:123943800-123949200	Weak transcription	Adipose Nuclei	Adipose
12	chr12:123943800-123949200	Weak transcription	Fetal Heart	heart
13	chr12:123943800-123949200	Weak transcription	Fetal Kidney	kidney
14	chr12:123943800-123949200	Weak transcription	Gastric	stomach
15	chr12:123943800-123949200	Weak transcription	NH-A	brain
16	chr12:123943800-123949400	Weak transcription	Brain Anterior Caudate	brain
17	chr12:123943800-123949400	Weak transcription	HSMM	muscle
18	chr12:123943800-123949600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:123943800-123949600	Weak transcription	Aorta	Aorta
20	chr12:123943800-123949600	Weak transcription	Brain Angular Gyrus	brain
21	chr12:123943800-123949600	Weak transcription	Esophagus	oesophagus
22	chr12:123943800-123949800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:123943800-123949800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:123943800-123949800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:123943800-123949800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:123943800-123949800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:123943800-123949800	Weak transcription	Left Ventricle	heart
28	chr12:123943800-123949800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:123943800-123949800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:123943800-123949800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:123943800-123949800	Weak transcription	Right Ventricle	heart
32	chr12:123943800-123956000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:123943800-123956400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr12:123943800-123958800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr12:123943800-123959600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:123943800-123959600	Weak transcription	Psoas Muscle	Psoas
37	chr12:123943800-123961200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:123944000-123947600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:123944000-123947600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:123944000-123948200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr12:123944000-123949000	Weak transcription	Placenta	Placenta
42	chr12:123944000-123949200	Weak transcription	Fetal Brain Female	brain
43	chr12:123944000-123949200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr12:123944000-123949200	Weak transcription	NHLF	lung
45	chr12:123944000-123949600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:123944000-123949800	Weak transcription	HMEC	breast
47	chr12:123944000-123950200	Weak transcription	HSMMtube	muscle
48	chr12:123944200-123949000	Weak transcription	Fetal Intestine Large	intestine
49	chr12:123944200-123949600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:123944200-123949600	Weak transcription	Colonic Mucosa	Colon

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