Variant report

Variant	rs13150783
Chromosome Location	chr4:48034488-48034489
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	chr4:48015687..48018286-chr4:48032689..48034980,2	K562	blood:
2	chr4:48034068..48036913-chr4:48142592..48144853,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1003873	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs13116684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13121957	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140968	0.85[AFR][1000 genomes]
rs13145218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13151608	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1567217	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs224799	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279965	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs321622	0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs321632	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs321634	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321635	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35085584	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695325	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55670663	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447609	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6812991	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674929	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13150783	CNGA1	cis	Thyroid	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
3	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
4	chr4:48024600-48043600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:48025400-48035000	Weak transcription	NHEK	skin
6	chr4:48026800-48045400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:48028200-48040800	Weak transcription	Gastric	stomach
8	chr4:48028200-48042600	Weak transcription	Placenta	Placenta
9	chr4:48028400-48037400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:48031600-48041800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:48032800-48045000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:48033000-48034800	Weak transcription	HMEC	breast
13	chr4:48033000-48037600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:48033000-48037600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:48033000-48037800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:48033000-48037800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:48033000-48045000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:48033200-48036000	Enhancers	Liver	Liver
19	chr4:48033400-48036400	Enhancers	Fetal Intestine Large	intestine
20	chr4:48033800-48034600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr4:48033800-48035000	Enhancers	Fetal Lung	lung
22	chr4:48033800-48035000	Enhancers	Hela-S3	cervix
23	chr4:48033800-48036200	Enhancers	Duodenum Mucosa	Duodenum
24	chr4:48034000-48034600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:48034000-48034800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:48034000-48034800	Enhancers	NH-A	brain
27	chr4:48034000-48035200	Enhancers	Adipose Nuclei	Adipose
28	chr4:48034000-48035200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr4:48034000-48036200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr4:48034000-48036600	Enhancers	Fetal Intestine Small	intestine
31	chr4:48034000-48038600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:48034200-48034600	Enhancers	Fetal Heart	heart
33	chr4:48034200-48034600	Enhancers	HSMMtube	muscle
34	chr4:48034200-48034800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:48034200-48035200	Weak transcription	Small Intestine	intestine
36	chr4:48034200-48035400	Enhancers	Stomach Mucosa	stomach
37	chr4:48034200-48035800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr4:48034200-48036200	Enhancers	HepG2	liver
39	chr4:48034200-48037600	Enhancers	GM12878-XiMat	blood
40	chr4:48034200-48049600	Weak transcription	Pancreas	Pancrea
41	chr4:48034400-48034600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr4:48034400-48034600	Enhancers	Psoas Muscle	Psoas
43	chr4:48034400-48034600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr4:48034400-48034600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr4:48034400-48035200	Enhancers	Fetal Brain Male	brain
46	chr4:48034400-48039400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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