Variant report

Variant	rs13121957
Chromosome Location	chr4:48043936-48043937
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	chr4:48018543..48020121-chr4:48043793..48046506,2	MCF-7	breast:
2	chr4:48043679..48046228-chr4:48047228..48049577,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198515	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13116684	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145218	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150783	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13151608	0.92[ASN][1000 genomes]
rs224799	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321632	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs321634	0.80[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	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695325	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55670663	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447609	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6812991	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674929	0.80[AFR][1000 genomes];0.95[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
rs13121957	CNGA1	cis	Thyroid	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
2	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
3	chr4:48026800-48045400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:48032800-48045000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:48033000-48045000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:48034200-48049600	Weak transcription	Pancreas	Pancrea
7	chr4:48036400-48046400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:48038000-48044600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:48038000-48044800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:48038000-48047800	Weak transcription	NHEK	skin
11	chr4:48038200-48044400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:48038200-48045200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:48038400-48044600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:48038600-48045200	Weak transcription	Fetal Heart	heart
15	chr4:48038600-48053000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:48039000-48045400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:48039400-48044800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:48039600-48044800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:48040400-48044400	Weak transcription	Fetal Intestine Large	intestine
20	chr4:48041000-48044000	Weak transcription	Primary B cells from cord blood	blood
21	chr4:48041000-48044600	Weak transcription	Fetal Intestine Small	intestine
22	chr4:48041200-48044400	Weak transcription	Liver	Liver
23	chr4:48041600-48053000	Weak transcription	HMEC	breast
24	chr4:48042200-48044800	Enhancers	HepG2	liver
25	chr4:48043000-48045200	Weak transcription	Stomach Mucosa	stomach
26	chr4:48043600-48044200	Enhancers	H9 Cell Line	embryonic stem cell
27	chr4:48043600-48044200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
28	chr4:48043800-48044200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:48043800-48045800	Flanking Active TSS	GM12878-XiMat	blood

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