Variant report

Variant	rs7299609
Chromosome Location	chr12:50024926-50024927
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:5)
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	POLR2A	chr12:50024479-50025167	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:50023976-50031574	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50024342..50028618-chr12:50029311..50035232,8	K562	blood:
2	chr12:50015886..50019957-chr12:50021996..50025809,6	K562	blood:
3	chr12:50023643..50026523-chr12:50135082..50136780,2	MCF-7	breast:
4	chr12:50023902..50034192-chr12:50133489..50138270,11	K562	blood:
5	chr12:49960687..49963976-chr12:50022315..50025513,4	K562	blood:

No data

Variant related genes	Relation type
PRPF40B	TF binding region
ENSG00000139644	Chromatin interaction
ENSG00000161791	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000187778	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1049986	0.84[MEX][hapmap]
rs10875968	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs11169063	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11169065	0.82[JPT][hapmap]
rs11169073	0.92[MEX][hapmap]
rs11169080	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs11169081	0.92[MEX][hapmap]
rs11169082	0.92[MEX][hapmap]
rs11169097	0.85[MEX][hapmap]
rs11169101	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169104	0.85[MEX][hapmap]
rs11169106	0.85[MEX][hapmap]
rs11169140	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs1150057	0.85[JPT][hapmap]
rs11833411	0.92[MEX][hapmap]
rs11834380	0.93[MEX][hapmap]
rs12299505	0.92[MEX][hapmap];0.82[AMR][1000 genomes]
rs12299513	0.82[AMR][1000 genomes]
rs12316284	0.85[MEX][hapmap]
rs12321819	0.92[MEX][hapmap]
rs1574326	0.85[MEX][hapmap]
rs17123808	0.92[MEX][hapmap]
rs17123981	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap]
rs1902330	0.82[JPT][hapmap]
rs2278068	1.00[JPT][hapmap]
rs2278069	0.92[MEX][hapmap]
rs2336058	0.85[MEX][hapmap]
rs2878532	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3815832	0.92[MEX][hapmap]
rs3887727	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs3887728	0.92[MEX][hapmap]
rs4073998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes]
rs4133070	0.85[MEX][hapmap]
rs4584654	0.85[MEX][hapmap]
rs59233136	0.85[EUR][1000 genomes]
rs61512987	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61616163	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7133398	1.00[CHB][hapmap]
rs7137976	0.85[MEX][hapmap]
rs7306877	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7309607	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7312658	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7688	0.85[MEX][hapmap]
rs7952734	0.85[MEX][hapmap]
rs7953911	0.92[MEX][hapmap]
rs7954994	0.85[MEX][hapmap];0.82[YRI][hapmap]
rs7955586	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs7956181	0.85[MEX][hapmap]
rs7962863	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7963954	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7965658	0.85[JPT][hapmap]
rs7970241	0.92[MEX][hapmap]
rs7973389	0.92[MEX][hapmap]
rs7975599	0.92[MEX][hapmap]
rs7975712	1.00[CHB][hapmap]
rs7977389	0.92[MEX][hapmap]
rs7979285	0.91[CEU][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs8626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs876889	0.92[MEX][hapmap]
rs897056	0.84[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	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
5	esv3417567	chr12:50024867-50025196	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50017000-50030600	Weak transcription	Fetal Heart	heart
2	chr12:50017200-50025600	Weak transcription	Fetal Lung	lung
3	chr12:50017400-50026600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:50017400-50027200	Weak transcription	Gastric	stomach
5	chr12:50017400-50027400	Weak transcription	Lung	lung
6	chr12:50017600-50035600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:50017800-50030600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:50017800-50036400	Weak transcription	Colonic Mucosa	Colon
9	chr12:50017800-50042200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:50018000-50025000	Weak transcription	Right Ventricle	heart
11	chr12:50018000-50025200	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:50018000-50025200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:50018000-50025200	Weak transcription	Fetal Intestine Large	intestine
14	chr12:50018000-50025400	Weak transcription	Brain Substantia Nigra	brain
15	chr12:50018000-50025800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:50018000-50027400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:50018000-50027600	Weak transcription	Aorta	Aorta
18	chr12:50018000-50028400	Weak transcription	Brain Angular Gyrus	brain
19	chr12:50018000-50030400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:50018000-50030400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:50018000-50030400	Weak transcription	Right Atrium	heart
22	chr12:50018000-50030600	Weak transcription	Adipose Nuclei	Adipose
23	chr12:50018000-50030600	Weak transcription	Fetal Kidney	kidney
24	chr12:50018000-50030600	Weak transcription	Stomach Mucosa	stomach
25	chr12:50018000-50030800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:50018000-50031000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:50018000-50031200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:50018000-50031800	Weak transcription	Liver	Liver
29	chr12:50018000-50035400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:50018000-50035600	Weak transcription	Left Ventricle	heart
31	chr12:50018000-50035800	Weak transcription	HSMMtube	muscle
32	chr12:50018000-50043000	Weak transcription	Psoas Muscle	Psoas
33	chr12:50018200-50025200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:50018200-50025400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:50018200-50025400	Weak transcription	Placenta	Placenta
36	chr12:50018200-50025400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr12:50018200-50025600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:50018200-50025600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:50018200-50025600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:50018200-50025600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:50018200-50025600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:50018200-50025600	Weak transcription	Ovary	ovary
43	chr12:50018200-50026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr12:50018200-50030400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:50018200-50030400	Weak transcription	HepG2	liver
46	chr12:50018200-50030800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:50018200-50033800	Weak transcription	Esophagus	oesophagus
48	chr12:50018400-50025200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:50018400-50025400	Weak transcription	Brain Anterior Caudate	brain
50	chr12:50018400-50025400	Weak transcription	Spleen	Spleen

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